The dynamic characteristics of elastic joints strongly affect the dynamic performance of a jointed structure. In order to study the performance of elastically jointed structure, a theoretical model of elastic joints has been developed based on the concept of dynamic contacts, in which the joint friction and clearance effects are included. A stochastic simulation technique is used to evaluate the system characteristics of jointed structures. In this paper, a time-domain system identification method is presented, which is applied to estimate the dynamic contact parameters of elastic joints and the eigenvalues of jointed structures. The identification system may use the data generated by using the theoretical model, or from experimental tests. The joint contact stiffness and contact damping are identified to be directional dependence of contact angles. The system natural frequencies and damping ratios are varied upon joint clearance variations. The simulation and experiment results are presented in this paper, and show comparisons.