When you stretch, it does a number of things to your muscles, tendons, and ligaments, to make them more flexible and do more with less pain. I always thought it just stretched the muscles to increase blood flow, but it actually causes material changes.
The water content changes as you stretch, making moving easier to flex and stretch.
Stem cells get activated and create differentiated cells that synthesize fibrillar collagens that increase stretchability.
There is a feedback loop that doesn't go all the way to your brain that gets accustomed to the stretching over time and ignores some of the pain.
The length of your muscle actually increases over time as well.
Amazing how the body has evolved to adapt in so many ways to simple changes in movement.
REF: https://academic.oup.com/cardiovascres/article/71/3/548/338681