Why my "let" variable does not clear the input field?

You can use two way to reset form by, html element in this case not two way bind with variable

isNumber = ''
form.number.value = isNumber;

or use

form.reset();

<!-- JS CODE  -->
const form = document.querySelector('.form');

form.addEventListener('submit' , e=> {
    e.preventDefault();
    let inNumber = form.number.value;

    let randomNumber = Math.ceil(Math.random() * inNumber);
    console.log(randomNumber);
    isNumber = ''
    form.number.value = isNumber;
    //form.reset();
})

<!-- HTML CODE  -->
<form action="" class="form">
    <input type="number" id="number">
    <input type="submit" name="" id="btn">
</form>

Since I'm not allowed to comment yet, here's what I noticed- If we set inNumber = form.number then inNumber.value = "" resets form.number.value. But inNumber = form.number.value doesn't perform the reset job with inNumber = "". Anybody knows the reason?

That's because form.number.value is a getter

let inNumber = form.number.value; this will give you the value not the setter i.e. not by reference. So doing isNumber = ''; will only change the value of isNumber not of form.number.value

And when you do form.number.value = '' it's a setter, hence it works.

Reference: w3schools - form.input.value

numbers are essentially copy-by-value when assigned to a variable. Which means the variable holds a copy of the value not a pointer to the forms value.

Later when you do

inNumber = '';

You are simply setting the variables value. You need to set the forms value to reset it:

form.number.value = '';

Alternately you can make a reference to the object holding the value

let inNumber = form.number;
// ...
inNumber.value = '';