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In factory-assembled structures, the bolted joint is the cause of local energy dissipation and flexibility, and its dynamics influences the dynamics of the whole structure. This paper puts forward a method to simulate the dynamics of bolted joint based on the thin-layer element (TLE) of nonlinear material. First, a finite-element model was built for an isolated bolted joint. Then, the tangential force-displacement curve of the bolted joint was obtained through an experiment on a universal testing machine (UTM) to reflect the features of the joint. On this basis, the response surface methodology (RSM) and the genetic algorithm (GA) were combined to identify the parameters of the material in the finite-element model. The simulated force-displacement curve agrees well with that measured through experiment. Our approach facilitates the precise prediction of the dynamics of factory-assembled structures with complex joints.