For the problem of insufficient flap rudder force of autonomous underwater vehicle (AUV) when navigating at low speed, a low-speed near-bottom stable control navigation scheme based on vertical thruster is presented. Based on the navigating speed, the thrust characteristics of the flap rudder and vector propeller are analyzed comparatively. Then the layout scheme of vertical thruster units in fore and aft grooves is designed. And AUV vertical motion control can be achieved by tuning PID (proportional-integral-derivative) parameters and optimizing control strategy. Finally, a large number of lake trials show that the vertical thruster can achieve better near-bottom fixed-depth sailing controllability at low speed compared with flap rudder thruster, and the vehicle can realize stable navigation with mean square errors of height within 0.1m and pitch within 0.5°.