When the larynx grows during puberty, it also drops lower in the throat. This makes the vocal tract (space between vocal chords and lips) longer, which changes how speech sounds.
The main acoustic measure that captures this physical difference is called F2, short for the second formant (See more information about formants here.) This graph shows F2 values for men and women in their "normal" speech:
Like pitch, though, this measure can be manipulated, for example by sticking your lips out (to lower F2 and sound masculine) or drawing them back into a smile shape (to raise F2 and sound feminine). Look at and listen to these examples of lip extension and retraction: