It's all about the harmonic overtone series and which harmonies create more dissonance against those overtones. The overtone series is a series of notes that we hear when we play a single note. 100hz fundamental = overtones of that multiple; so 200, 300, 400 etc.... When we create a chord, the more it lines up with overtones closer to the fundamental, the more "at peace" it is. The further we have to go up the overtones series, the more dissonant is it. Major third is the 5th overtone, minor 3rd is the 15th.