This paper thoroughly studies a control system with control allocation for a manned submersible in deep sea being developed in China. The proposed control system consists of a neural-network-based direct adaptive controller and a dynamic control allocation module. A control energy cost function is used as the optimization criteria of the control allocation module, and weighted pseudo-inverse is used to find the solution of the control allocation problem. In the presence of bounded unknown disturbance and neural networks approximation error, stability of the closed-loop control system of manned submersible is proved with Lyaponov theory. The feasibility and validity of the proposed control system is further verified through experiments conducted on a semi-physical simulation platform for the manned submersible in deep sea.