For the fact that the ship propeller has a strict requirement for the running accuracy of the water lubricated rubber bearing system (WLRBS), a finite element contact model of the WLRBS was established. The effects of the rubber liner's hardness and thickness on the runout of the WLRBS with straight or spiral grooves were analyzed, and a way of controlling the runout was put forward. The research results indicate that the value of the runout increases with the decrease of the rubber hardness, while increases with the increase of the rubber thickness. And the runout of the shaft is relatively small when the hardness varies between 85~95 shore A. The thickness of rubber should be designed as thin as possible with ensuring the groove dimension. Besides, the runout of the WLRBS with spiral grooves is smaller than that with straight grooves. Therefore, scientific and reasonable design of the geometric structure and the hardness of the rubber liner can significantly reduce the value of the runout and improve the running accuracy.