In order to reveal vibration characteristics of rolling element bearing in depth, deep groove ball bearing 6304 was taken as the investigation object and bearing-pedestal system flexible multibody finite element model for 3D contact nonlinear dynamic problem was established taking account of the deformation of the pedestal and races. Aiming at nonlinear characteristics of bearing stiffness, a method of calculating time varying stiffness of bearing was put forward and time varying characteristics during running process was studied. Based on the consideration of nonlinear factors such as time varying stiffness, radial clearance, nonlinear contact, ect., nonlinear numerical simulation of running process was made and vibration accelerations on inner race, outer race and rolling element of bearing were obtained, vibration features of inner-race, outer-race and rolling element in time domain and frequency domain were analyzed, and the effect of radial clearance on the vibration characteristics of bearing was also studied. The research results could provide theoretical basis for reducing bearing’s vibration and noise, also for running state monitoring.