Ships navigating in the water need to consider their safety first, and the abnormal sinking amount of the ship will be a great threat to the navigation safety of the ship. In this paper, the relationship between hydrodynamic parameters and ship sinking amount is studied in order to realize the reasonable control of the ship by setting different hydrodynamic parameters so as to ensure the safety of ship navigation. Through Taylor’s formula to calculate the hydrodynamic parameters of the ship navigation, and through the combination of potential flow theory and boundary conditions, finally using Green’s function method in the surface element method, it is calculated that the sinking amount of the ship from hydrodynamic parameter 35000 to hydrodynamic parameter 3200000 is a gently increasing trend, and in the case of h/d=2.5, the ship’s speed Fn=0.25, the ship’s sinking amount appears to be oscillating changes.