The accuracy and efficiency are hardly acquired together in most wear analysis methods. Especially, the effect of contact stiffness is rarely considered in the wear analysis process. Therefore, a wear analysis method of clearance joint considering the effect of contact stiffness is presented. Massless link and spring damping (MLSD) model is used to conduct dynamic analysis of clearance joint system considering the effect of contact stiffness. The nonsymmetric Winkler surface model is taken to compute the contact pressure distribution. The Archard wear theory is adopted to calculate the wear amount of contact surface. The surface contour changes with the wear calculation results over time. Then, the dynamic wear trend of clearance joint is acquired. The analysis results reveal that when the contact stiffness coefficients are small, the effect on wear results of clearance joint becomes obvious and turns to a different change trend with the change of rotation speed. The effect of different contact stiffness is fully considered and the wear analysis results are obtained with a high calculation accuracy and efficiency. The paper's work can provide guidance for the design of same type mechanisms, and have great theoretical significance and application value to the lifetime prediction of clearance joint system.