Abstract: The 2D plane method is not accurate enough to analyze the effect on propulsion shaft system by hull deformation, therefore, the 3D FE model of a bulk carrier was conducted. The wave pressure was calculated and loaded automatically based on Patran command language (PCL). The deformations of ship construction in various sea waves were calculated and the effect on bearing load was analyzed. The result shows that the deflection of hull under shaft line is small in and under the sea state 4. The deflection of hull under shaft line is increased by sea state. And it is more than 4 mm in the sea state 8, affecting the shaft bearing load enormously. The deflection of hull under shaft line in vertical, horizontal and longitudinal directions is increased when the course heading is 30°.