General method is directly used the measured frequency response functions (FRFs) to identify the characteristics of bolted joints. However, the system’s ill-posed problems arise from the measurement error, the noise effect and the measurement at the mechanical joints may be obstructed by joining mechanisms. A new identification method with FRFs is developed to avoid the ill-posed problem. Firstly, the whole structure composed of substructures and bolted joints finite element model is established, the value range of equivalent stiffness and equivalent damping are obtained by the relationship between the parameters of bolted joints and the normalized frequency. The averages of the value range of equivalent stiffness and equivalent damping are used for the initial value of the bolted joints model, using the minimal FRFs calculation error of experiment and simulation as the objective. Finally, the equivalent stiffness and equivalent damping of bolted joints are obtained. From the results of simulation, experiment and Ref [16], results show that the proposed method can significantly improve the accuracy of identification.