Who controls the military in the US?

No, in reality the US Government is in control of the US Military, the government determines the total size of the military, its budget and salaries as well as a lot more like research and development. The heads of the various military branches have the responsibility of advising the commander in chief, concerning military issues, and proposes to the Secretary of Defense and to the US president miliary requirements and what types of military equipment is needed to protect the US.