Abstract: For the rolling element bearing rotor system, the bearing housings may deflect due to the limitation of machining precision and installation one. The bearing housing deflection will change the bearing’s stiffness and then influence the vibration performance of the rotor system. In this work, a rotor supported by two cylindrical roller bearings was investigated. The load and deformation between the roller and the raceways of the bearing was analyzed, and the bending deformation of the rotor was studied as well. An analytical model was established for calculating the radial stiffness and angular stiffness of the bearing with considering the bearing housing deflections. Consequently, a vibration model which considers the influences of the bearing housing deflections was developed for the bearing rotor system. With a calculation example, the influences of the housing deflection angles on the vibration performance of bearing rotor system were computed numerically and a series of conclusions were obtained and explained.