This paper mainly studies the large dive depth of underactuated AUV’s control problem. In order to solve the problem of external time-varying interferences in the process of underactuated AUV dive at large depth, this paper first divides the interferences into the current interferences and the buoyancy interferences according to AUV depth changes. Then the mathematical model is built and the adaptive law is designed for the external interferences. Aiming at the non-linear tracking control of underactuated AUV and the jump of motion parameters caused by non-smooth tracking trajectory, this paper proposes a backstepping control method based on bio-inspired model and uses the virtual velocity variables instead of the attitude errors. Finally, a three-dimensional trajectory tracking controller is designed from the view point of dynamics, which improves system robustness and tracking control accuracy. The stability of the proposed method is proved by Lyapunov function. The simulation results prove the effectiveness of the proposed method.