Array of arrays (jagged arrays) are faster than multi-dimensional arrays and can be used more effectively. Multidimensional arrays have nicer syntax.

If you write some simple code using jagged and multidimensional arrays and then inspect the compiled assembly with an IL disassembler you will see that the storage and retrieval from jagged (or single dimensional) arrays are simple IL instructions while the same operations for multidimensional arrays are method invocations which are always slower.

Consider the following methods:

static void SetElementAt(int[][] array, int i, int j, int value)
{
    array[i][j] = value;
}

static void SetElementAt(int[,] array, int i, int j, int value)
{
    array[i, j] = value;
}

Their IL will be the following:

.method private hidebysig static void  SetElementAt(int32[][] 'array',
                                                    int32 i,
                                                    int32 j,
                                                    int32 'value') cil managed
{
  // Code size       7 (0x7)
  .maxstack  8
  IL_0000:  ldarg.0
  IL_0001:  ldarg.1
  IL_0002:  ldelem.ref
  IL_0003:  ldarg.2
  IL_0004:  ldarg.3
  IL_0005:  stelem.i4
  IL_0006:  ret
} // end of method Program::SetElementAt

.method private hidebysig static void  SetElementAt(int32[0...,0...] 'array',
                                                    int32 i,
                                                    int32 j,
                                                    int32 'value') cil managed
{
  // Code size       10 (0xa)
  .maxstack  8
  IL_0000:  ldarg.0
  IL_0001:  ldarg.1
  IL_0002:  ldarg.2
  IL_0003:  ldarg.3
  IL_0004:  call       instance void int32[0...,0...]::Set(int32,
                                                           int32,
                                                           int32)
  IL_0009:  ret
} // end of method Program::SetElementAt

When using jagged arrays you can easily perform such operations as row swap and row resize. Maybe in some cases usage of multidimensional arrays will be more safe, but even Microsoft FxCop tells that jagged arrays should be used instead of multidimensional when you use it to analyse your projects.

A multidimensional array creates a nice linear memory layout while a jagged array implies several extra levels of indirection.

Looking up the value jagged[3][6] in a jagged array var jagged = new int[10][5] works like this: Look up the element at index 3 (which is an array) and look up the element at index 6 in that array (which is a value). For each dimension in this case, there's an additional look up (this is an expensive memory access pattern).

A multidimensional array is laid out linearly in memory, the actual value is found by multiplying together the indexes. However, given the array var mult = new int[10,30], the Length property of that multidimensional array returns the total number of elements i.e. 10 * 30 = 300.

The Rank property of a jagged array is always 1, but a multidimensional array can have any rank. The GetLength method of any array can be used to get the length of each dimension. For the multidimensional array in this example mult.GetLength(1) returns 30.

Indexing the multidimensional array is faster. e.g. given the multidimensional array in this example mult[1,7] = 30 * 1 + 7 = 37, get the element at that index 37. This is a better memory access pattern because only one memory location is involved, which is the base address of the array.

A multidimensional array therefore allocates a continuous memory block, while a jagged array does not have to be square, e.g. jagged[1].Length does not have to equal jagged[2].Length, which would be true for any multidimensional array.

Performance

Performance wise, multidimensional arrays should be faster. A lot faster, but due to a really bad CLR implementation they are not.

 23.084  16.634  15.215  15.489  14.407  13.691  14.695  14.398  14.551  14.252 
 25.782  27.484  25.711  20.844  19.607  20.349  25.861  26.214  19.677  20.171 
  5.050   5.085   6.412   5.225   5.100   5.751   6.650   5.222   6.770   5.305 

The first row are timings of jagged arrays, the second shows multidimensional arrays and the third, well that's how it should be. The program is shown below, FYI this was tested running mono. (The windows timings are vastly different, mostly due to the CLR implementation variations).

On windows, the timings of the jagged arrays are greatly superior, about the same as my own interpretation of what multidimensional array look up should be like, see 'Single()'. Sadly the windows JIT-compiler is really stupid, and this unfortunately makes these performance discussions difficult, there are too many inconsistencies.

These are the timings I got on windows, same deal here, the first row are jagged arrays, second multidimensional and third my own implementation of multidimensional, note how much slower this is on windows compared to mono.

  8.438   2.004   8.439   4.362   4.936   4.533   4.751   4.776   4.635   5.864
  7.414  13.196  11.940  11.832  11.675  11.811  11.812  12.964  11.885  11.751
 11.355  10.788  10.527  10.541  10.745  10.723  10.651  10.930  10.639  10.595

Source code:

using System;
using System.Diagnostics;
static class ArrayPref
{
    const string Format = "{0,7:0.000} ";
    static void Main()
    {
        Jagged();
        Multi();
        Single();
    }

    static void Jagged()
    {
        const int dim = 100;
        for(var passes = 0; passes < 10; passes++)
        {
            var timer = new Stopwatch();
            timer.Start();
            var jagged = new int[dim][][];
            for(var i = 0; i < dim; i++)
            {
                jagged[i] = new int[dim][];
                for(var j = 0; j < dim; j++)
                {
                    jagged[i][j] = new int[dim];
                    for(var k = 0; k < dim; k++)
                    {
                        jagged[i][j][k] = i * j * k;
                    }
                }
            }
            timer.Stop();
            Console.Write(Format,
                (double)timer.ElapsedTicks/TimeSpan.TicksPerMillisecond);
        }
        Console.WriteLine();
    }

    static void Multi()
    {
        const int dim = 100;
        for(var passes = 0; passes < 10; passes++)
        {
            var timer = new Stopwatch();
            timer.Start();
            var multi = new int[dim,dim,dim];
            for(var i = 0; i < dim; i++)
            {
                for(var j = 0; j < dim; j++)
                {
                    for(var k = 0; k < dim; k++)
                    {
                        multi[i,j,k] = i * j * k;
                    }
                }
            }
            timer.Stop();
            Console.Write(Format,
                (double)timer.ElapsedTicks/TimeSpan.TicksPerMillisecond);
        }
        Console.WriteLine();
    }

    static void Single()
    {
        const int dim = 100;
        for(var passes = 0; passes < 10; passes++)
        {
            var timer = new Stopwatch();
            timer.Start();
            var single = new int[dim*dim*dim];
            for(var i = 0; i < dim; i++)
            {
                for(var j = 0; j < dim; j++)
                {
                    for(var k = 0; k < dim; k++)
                    {
                        single[i*dim*dim+j*dim+k] = i * j * k;
                    }
                }
            }
            timer.Stop();
            Console.Write(Format,
                (double)timer.ElapsedTicks/TimeSpan.TicksPerMillisecond);
        }
        Console.WriteLine();
    }
}

Simply put multidimensional arrays are similar to a table in DBMS.
Array of Array (jagged array) lets you have each element hold another array of the same type of variable length.

So, if you are sure that the structure of data looks like a table (fixed rows/columns), you can use a multi-dimensional array. Jagged array are fixed elements & each element can hold an array of variable length

E.g. Psuedocode:

int[,] data = new int[2,2];
data[0,0] = 1;
data[0,1] = 2;
data[1,0] = 3;
data[1,1] = 4;

Think of the above as a 2x2 table:

1 | 2
3 | 4

int[][] jagged = new int[3][]; 
jagged[0] = new int[4] {  1,  2,  3,  4 }; 
jagged[1] = new int[2] { 11, 12 }; 
jagged[2] = new int[3] { 21, 22, 23 }; 

Think of the above as each row having variable number of columns:

 1 |  2 |  3 | 4
11 | 12
21 | 22 | 23

Multi-dimension arrays are (n-1)-dimension matrices.

So int[,] square = new int[2,2] is square matrix 2x2, int[,,] cube = new int [3,3,3] is a cube - square matrix 3x3. Proportionality is not required.

Jagged arrays are just array of arrays - an array where each cell contains an array.

So MDA are proportional, JD may be not! Each cell can contains an array of arbitrary length!

I thought I'd chime in here from the future with some performance results from .NET 5, seen as that will be the platform which everyone uses from now on.

These are the same tests that John Leidegren used (in 2009).

My results (.NET 5.0.1):

  Debug:
  (Jagged)
  5.616   4.719   4.778   5.524   4.559   4.508   5.913   6.107   5.839   5.270
  
  (Multi)
  6.336   7.477   6.124   5.817   6.516   7.098   5.272   6.091  25.034   6.023
  
  (Single)
  4.688   3.494   4.425   6.176   4.472   4.347   4.976   4.754   3.591   4.403


  Release(code optimizations on):
  (Jagged)
  2.614   2.108   3.541   3.065   2.172   2.936   1.681   1.724   2.622   1.708

  (Multi)
  3.371   4.690   4.502   4.153   3.651   3.637   3.580   3.854   3.841   3.802

  (Single)
  1.934   2.102   2.246   2.061   1.941   1.900   2.172   2.103   1.911   1.911

Ran on a a 6 core 3.7GHz AMD Ryzen 1600 machine.

It looks as though the performance ratio is still roughly the same. I'd say unless you're really optimizing hard, just use multi-dimensional arrays as the syntax is slightly easier to use.

Jagged arrays are arrays of arrays or arrays in which each row contains an array of its own.

These arrays can have lengths different than those in the other rows.

Declaration and Allocation an Array of Arrays

The only difference in the declaration of the jagged arrays compared to the regular multidimensional array is that we do not have just one pair of brackets. With the jagged arrays, we have a pair of brackets per dimension. We allocate them this way:

int[][] exampleJaggedArray;
jaggedArray = new int[2][];
jaggedArray[0] = new int[5];
jaggedArray[1] = new int[3];

The Initializing an array of arrays

int[][] exampleJaggedArray = {
new int[] {5, 7, 2},
new int[] {10, 20, 40},
new int[] {3, 25}
};

Memory Allocation

Jagged arrays are an aggregation of references. A jagged array does not directly contain any arrays, but rather has elements pointing to them. The size is unknown and that is why CLR just keeps references to the internal arrays. After we allocate memory for one array-element of the jagged array, then the reference starts pointing to the newly created block in the dynamic memory.

The variable exampleJaggedArray is stored in the execution stack of the program and points to a block in the dynamic memory, which contains a sequence of three references to other three blocks in memory; each of them contains an array of integer numbers – the elements of the jagged array:

Using a test based on the one by John Leidegren, I benchmarked the result using .NET 4.7.2, which is the relevant version for my purposes and thought I could share. I originally started with this comment in the dotnet core GitHub repository.

It appears that the performance varies greatly as the array size changes, at least on my setup, 1 processor xeon with 4physical 8logical.

w = initialize an array, and put int i * j in it. wr = do w, then in another loop set int x to [i,j]

As array size grows, multidimensional appears to outperform.

Update: last two tests with double[,] instead of int[,]. The difference appears significant considering the errors. With int, ratio of mean for jagged vs md is between 1.53x and 1.86x, with doubles it is 1.88x and 2.42x.