Well, a lot of harmonies are built on top of the harmonic series.
See https://www.youtube.com/watch?v=Wx_kugSemfY
And tuning is all about 'numerical puns', similar to how eg 2^10 ~ 10^3, but for perfect fifths and octaves etc.
Of course, our physiology and culture is a bit too complicated and convoluted to understand everything about music from first principles like this. So most of the time you are better off learning (and treating) music as music instead of as applied math or physics.