For example, I have gameObject with two box collider2D components. I want to change Physics2D Material by script for only specific one of these colliders. But how I can differ these same colliders in script?
If you know beforehand which one you want to change, the easiest would be to add a reference to it in your script:
public Collider2D colliderToCange;
and then change it when you need to.
As an alternative, you can put the two colliders in different child objects.