In order to ensure the safety of AUV (Autonomous Underwater Vehicle) operation on the complex seafloor, it is necessary to analyze the hydrodynamic effect of the seafloor on the AUV. In this paper, a multi-block dynamic hybrid grid method was used to simulate the hydrodynamic performance of an AUV sailing straight through complex seafloor in hilly terrain with different slopes, and the histories of unsteady drag, suction force, and trim moment of the AUV were obtained. The results show that the AUV drag and suction force increase as the bow of the AUV moves near the top of the hill, and the AUV drag and suction decrease and oscillate as it leaves the hill. For different hill heights, the steeper the hill slope, the greater the increase in drag. The greater the width of the hill, the greater the effect on drag and suction. The suction force is coupled by the slope and width, and its maximum value occurs at the top of the 15° slope. Tail trim is also shown as the AUV passing through the hill, and the trend of the tail trim changes is the same as that of the suction force, but the frequency of oscillation increases. The research conducted in this paper provides good reference for the safety and maneuverability of AUVs navigating close to the seafloor.