In this article, a composite control scheme, consisting of the conditional disturbance compensation controller and control allocation, is proposed for a manned submersible vehicle (MSV). First of all, a composite disturbance estimation method combining nonlinear disturbance observer (NDOB) and fuzzy logic system (FLS) is used to estimate the external disturbance and model uncertainty, which can acquire better accuracy than the conventional estimation method with a single NDOB. Second, a new disturbance characterization index (DCI) is proposed for the MSV, which not only indicates whether the disturbance/uncertainty is beneficial to MSV, but also reflects the beneficial degree of the disturbance/uncertainty. A conditional disturbance compensation controller is then developed on the basis of DCI, where the detrimental disturbance/uncertainty is eliminated and the favorable disturbance/uncertainty is reserved to further improve the system performance. Furthermore, a control allocation scheme is proposed to solve the overactuated problem of MSV, which can save energy consumption of the thruster system by making full use of the azimuth thrusters in MSV. Finally, the semiglobal asymptotic stability of the MSV system is rigorously analyzed. The effectiveness of the proposed composite control scheme is also verified by the simulations.