The operation of underwater vehicles in deep waters is a very challenging task. The use of AUVs (Autonomous Underwater Vehicles) is the preferred option for underwater exploration activities. They can be autonomously navigated and controlled in real time underwater, which is only possible with precise spatio-temporal information. Navigation and positioning systems based on LBL (Long-Baseline) or USBL (Ultra-Short-Baseline) systems have their own characteristics, so the choice of system is based on the specific application scenario. However, comparative experiments on AUV navigation and positioning under both systems are rarely conducted, especially in the deep sea. This study describes navigation and positioning experiments on AUVs in deep-sea scenarios and compares the accuracy of the USBL and LBL/SINS (Strap-Down Inertial Navigation System)/DVL (Doppler Velocity Log) modes. In practice, the accuracy of the USBL positioning mode is higher when the AUV is within a 60° observation range below the ship; when the AUV is far away from the ship, the positioning accuracy decreases with increasing range and observation angle, i.e., the positioning error reaches 80 m at 4000 m depth. The navigational accuracy inside and outside the datum array is high when using the LBL/SINS/DVL mode; if the AUV is far from the datum array when climbing to the surface, the LBL cannot provide accurate position calibration while the DVL fails, resulting in large deviations in the SINS results. In summary, the use of multi-sensor combination navigation schemes is beneficial, and accurate position information acquisition should be based on the demand and cost, while other factors should also be comprehensively considered; this paper proposes the use of the LBL/SINS/DVL system scheme.