This paper investigates the time-varying formation containment problem for multiple autonomous underwater vehicles (MAUVs) system subject to actuator faults in three-dimensional space. The leader AUVs are required to track the virtual leader AUV with time-varying offset vectors, and at the same time the follower AUVs are demanded to converge into the convex hull formed by the leader AUVs. The extended state observers (ESOs) are designed to estimate the external disturbances and unknown nonlinearities of MAUVs system in real time, hence ensuring the anti-disturbance ability of MAUVs system. The tracking differentiators (TDs) are developed so as to avoid the differential explosion issues caused by the derivatives of the virtual control laws. The distributed formation containment control laws are put forward for compensating the impacts of unknown bounded actuator bias fault and loss of actuator effectiveness fault based on adaptive control strategy. Furthermore, the stability of MAUVs system is demonstrated by means of Lyapunov stability theory. At last, a numerical simulation is presented to confirm the effectiveness of the proposed method.