A general dynamic modeling method of ball bearing–rotor systems is proposed. Gupta's bearing model is applied to predict the rigid body motion of the system considering the three-dimensional motions of each part (i.e., outer ring, inner ring, ball, and rotor), lubrication tractions, and bearing clearances. The finite element method is used to model the elastic deformation of the rotor. The dynamic model of the whole ball bearing–rotor system is proposed by integrating the rigid body motion and the elastic vibration of the rotor. An experiment is conducted on a test rig of rotor supported by two angular contact ball bearings. The simulation results are compared with the measured vibration responses to validate the proposed model. Good agreements show the accuracy of the proposed model and its ability to predict the dynamic behavior of ball bearing–rotor systems. Based on the proposed model, vibration responses of a two bearing–rotor system under different bearing clearances were simulated and their characteristics were discussed. The proposed model may provide guidance for structural optimization, fault diagnosis, dynamic balancing, and other applications.