A comparative study of dynamic analysis for planar multibody systems with ball bearing joints is conducted in this study. The transmission mechanism is used as the exemplar case for illustrating the effect of ball bearing joints on the dynamic behavior of multibody systems. To reflect the energy loss, the models of continuous contact force and modified Coulomb’s friction are considered in the kinematic equations for the multibody system with ball bearing joint. With this, the dynamic characteristics of the mechanism are studied. Meanwhile, an experimental platform is built to generate the test data for demonstrating the effectiveness and correctness of the proposed method. Moreover, the effects of driving speed and clearance size on the dynamic behavior of the multibody system are investigated. The numerical results indicate that the dynamic behavior of the mechanical system is sensitive to the variation of the design parameters and the selection of parameters can affect greatly the accuracy of the mechanism with clearance joints.