In this paper, a model was developed to study the effects of rotor and support flexibilities on the performance of rotor-bearing-housing system. The system is composed of a flexible rotor and two supporting deep-groove ball bearings mounted in flexible bearing housings. The dynamics of the ball bearings were simulated using an existing dynamic bearing model, which was developed using the discrete element method (DEM). The explicit finite element method (EFEM) was used to model the flexibilities of the rotor and bearing support. In order to combine the dynamic bearing model with finite element rotor and support system, new contact algorithms were developed for the interactions between the various components in the system. The Total Lagrangian formulation approach was applied to decrease the computational effort needed for modeling the rotor-bearing-housing system. The combined model was then used to investigate the effects of bearing clearances and housing clearances. And it was found that, as the rotor is deformed due to external loading, the clearances have a significant impact on the bearing varying compliance motion and reaction moments. Results also show that deformation of the flexible housing depends on the total force and moment generated within the bearing due to rotor deformation. The first critical speed of rotor was simulated to investigate the unbalance response of the rotor-bearing system. It was demonstrated that rotor critical speed has a significant effect on inner race displacement and reaction moment generated at bearing location.