Well, your question in a bit unclear as you haven’t mentioned the particular watch because currently Apple watch 3 (GPS) is compatible with iPhone 5s models and the Apple watch 3 (GPS + Cellular) is compatible with iPhone 6 and models which were launched by Apple Corporation later.

iPhone SE was launched after the iPhone 6s on 31st March 2016 and has the almost similar feature as in the iPhone 6s so you don’t need to worry because iPhone SE is compatible with the Apple watch series.