Water lubricated stern bearings (WLSBs) are the critical component of ship propulsion system and have important effect on navigation safety. Operating temperature plays a main role on the performance of WLSBs. This paper aims to investigate the effect of operating conditions on bearing temperature characteristics under hydrodynamic lubrication. A novel CFD simulation method developed to improve calculation accuracy. Finite difference method was used to decrease the error of geometric modeling while the experiment and experimental correction formula were exploited to obtain improved boundary conditions. Based on the new method, the effects of operating conditions on temperature characteristics for two typical WLSBs were studied, and mechanisms of bearing temperature field evolution were discussed. Results show that the max friction coefficient appears when bearings are in low velocity and low load condition. Total heat flux density is a function of linear velocity, pressure and friction coefficient. Max temperature of bearing at 0.4 MPa decrease along with increased velocity, while decrease first and then increase at 0.2 MPa. Moreover, peak temperature appears at eccentric side and beyond minimum water film thickness position about 4–40°. High temperature area mainly located at the position of 80–140° in circumferential direction and 0.2–0.13 m in axial direction. With the increase of inlet water velocity, the max temperature of bearing changes slightly. It is appropriate to set the inlet velocity at 2 m/s to obtain better cooling performance. This work can provide theoretical basis for the operation monitoring of WLSBs and the development of new materials.