To solve the trajectory control problem exactly for Autonomous Underwater Vehicle (AUV) under external marine environment disturbance. Robust H∞ controller is proposed for underactuated AUV trajectory tracking system. The three dimensional trajectory controller was decomposed into the horizontal plane and vertical plane. After that, the dynamic models with the influence of linearization errors, uncertainties and external disturbance were proposed in the horizontal plane and vertical plane respectively. Then the heading controller and pitch controller were designed based on the robust H∞ theory. The simulation result shows that the method can overcome outside disturbance of constant ocean current and ensure the precision track, where the tracking error can converge to zero. The robust H∞ controller designed for AUV is effectively and can be applied to the tracking system.