To address the issue of poor rudder effectiveness and difficulty in depth control for underwater vehicles at low speeds, a novel depth control algorithm based on the combination of rudder and auxiliary thruster is proposed. The algorithm utilizes the vertical motion model of the underwater vehicle to design a linear sliding mode controller (SMC) for depth and pitch angle regulation. Parameters of the SMC are tuned using pole placement, which reduces the number of parameters requiring adjustment. Then, a nonlinear disturbance observer is designed to estimate and compensate for external disturbances and coupling disturbances affecting depth and pitch angles. This observer replaces the discontinuous term in the sliding mode control, thereby reducing controller chattering while improving control accuracy. Finally, a thrust allocation matrix combining rudder and auxiliary thruster is constructed, and Lagrange multipliers are employed to derive an analytical solution for thrust distribution between the rudder and auxiliary thruster. This approach significantly reduces optimization computation time, making it suitable for practical engineering applications. Simulation results demonstrate that the proposed control algorithm effectively enhances the vehicle’s control capability at low speeds while reducing propeller energy consumption compared to using vertical thrusters alone.