Boys develop a deep voice as part of the process of puberty, it is generally a change that occurs around half way through the process. The main hormone responsible for this change is testosterone, which stimulates the enlargement of the larynx (also called the Adam's Apple or voice box).

Androgen's such as Testosterone not only give a boy a deeper voice but sets him up for sexual reproduction too.
Testosterone is the male hormone that begins to spread around the body during puberty in a boy. Besides a deep voice it brings pubic hair and growth to the penis, testicles, arms, legs, feet, hands. You name it !