In this paper, the effects on dynamic characteristics of a mechanism with clearance driven by harmonic drive, considering the flexibility of harmonic gear, were investigated. Firstly, the contact model of a mechanism with clearance driven by harmonic drive was established by using the nonlinear spring-damp model. Then, a slider-crank mechanism with clearance was simulated. The result showed that harmonic drive and flexibility of mechanical parts had cushioning effect of collisions for clearance. The cushioning effect was not obvious when the stiffness of mechanical parts was high, while the reduction of stiffness of mechanical parts would result in large deformation during the run which would influence the mechanical properties of the mechanism. It set a theoretical foundation for the use of harmonic drive in mechanisms with clearance.