The Autonomous Underwater Vehicle (AUV) is used for underwater exploration of the sea floor. The AUV uses an Inertial Navigation System (INS) to recognize its position in the water, through the position estimation error of the INS increases with time. As the INS accumulated error increases, the success rate of the task decreases. Global Positioning System (GPS) is used for all kinds of vehicles moving on the ground or in the air; however, it cannot be widely utilized in water because radio signals cannot penetrate into the deep water. Therefore, how to eliminate the INS error is an important topic for the AUV. In this study, we propose a stereo-vision-based navigation system applied to the AUV to reset the integrated INS error. The experiments of the AUV navigation and returning to the docking station were conducted in the test tank by means of the INS and the stereo-vision system. The experimental results show that our proposed method is capable of docking the AUV and resetting the integrated INS error.