In order to obtain the precise physical parameters of the flexible joint, a parameter identification method based on system resonance and anti-resonance characteristics is proposed. Firstly, the mathematical model of the flexible joint is established to derive the mathematical relationship between the resonance and anti-resonance frequency characteristics of the flexible joint and the parameters to be identified. Based on this relationship, an error regression model is established. The input/output data are collected under different load conditions through experiments, the resonance and anti-resonance frequencies of the system and their corresponding amplitudes are calculated and substituted into the regression model, and the parameters are solved by the least squares (LS) method. Finally, the proposed method is compared with the general method of fitting with frequency domain characteristics both in simulation and experiments. The results show that the average accuracy of parameter identification is improved from 75.34% to 90.35%, and the variance is decreased from 25.34% to 8.07% in the case of noises by the proposed method, which verify the feasibility and effectiveness of the proposed method.