The effect of clamping forces on a motor–toggle mechanism is dynamically modeled in this paper, and the clamping unit is presented by a simple spring-damper model. Based on real practical applications, the impact force model (IFM) associated with clamping effectiveness must be considered during the process of clamping. A two-stage identification method is also needed to develop for validating dynamic responses of the unclamping and clamping motions. The real-coded genetic algorithm (RGA) is employed to obtain system's parameters by two different fitness functions. The RGA feasibility is verified by the assigned parameters in numerical simulations, and then applied to the experimental physical model. Finally, numerical simulations and experimental results showed good agreement, and the proposed two-stage identification method described in this paper is found to be both better and necessary for the mechatronic system with a clamping unit.