With the popularity of the water lubricated rubber stern bearing, researches around rubber bearings are becoming more and more popular in recent years. This paper built a 3D numerical model of water-lubricated rubber stern bearing and did both free boundary and constraint modal analysis using finite element software ANSYS. The results show that free modes of water-lubricated rubber stern bearing are correlating with the constraint modes. The natural frequency distributes intensely in low frequency and the modal shapes mainly focus in the inner lining. Along with mode order increased, the mode shapes become more complicated. The mode shapes mainly embodies in the inner lining.