as @ilke444 commented, you can add \tag{1} to end of each line. And if you need refer to one specific line, you can add label in line.
.. math::
\begin{align}
100 + x &= y \label{a} \tag{1} \\
\frac{y}{x} &\ge 1.3 \label{b} \tag{2} \\
(100+x)-(100+x)z &= y \label{c} \tag{3}
\end{align}
output:

So you can refer it like this:
refer it inline :math:`\ref{a}`
refer it for single line:
.. :math:: \ref{a}
Notice: label should be unique, otherwise output will not be rendered.
update: upgrade mathjax in sphinx now support auto numbering line as latex.
open index.html in _build directory and change mathjax script
<script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
change it to:
<script>
window.MathJax = {
tex: {
tags: "ams"
}
};
</script>
<script
type="text/javascript"
id="MathJax-script"
async
src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"
></script>
Now all line in align block will auto numbering.
related doc: Automatic Equation Numbering
Why python-sphinx behavior like this?
source code for numbering in sphinx
Python-Sphinx handle every math block as whole and assign numbering for whole math block. When generating html, it will ignore numbering within math block, and leave it to math rendering library (default is MathJax).
So indeed, the problem is why Mathjax don't support auto numbering line in align block, so you can refer to this answer
How to number and reference multiline equations?
By now, the only way is add tag to each line :(, no automatic way.
BTW
If you only want one label for whole math block
As far as I know, python-sphinx provides option for generate number for each math block (by using :label:
.. math::
\begin{align}
100 + x &= y \\
\frac{y}{x} &\ge 1.3 \\
(100+x)-(100+x)z &= y
\end{align}
:label: abc
output

Label (2) because sequence number is generated due to its position in whole document.
And you can refer to it by
refer to it by :eq:`abc`