The assembly error of flexible joints and the change in joint stiffness during movement make the actual value of joint parameters inconsistent with the given value, which affects the joint control accuracy. In order to suppress the influence of parameters error, a parameters identification method for flexible joint combined offline identification and online compensation is proposed. First, the offline identification model of inertia, mass, and damping and the online identification model of joint stiffness are established, respectively. Then, a hybrid tracking differentiator based on an improved Sigmoid function is designed to track the differential signals of joint motion parameters, and the Lyapunov function is designed to prove its convergence. The adaptive differential evolution is used as the identification algorithm, and the improved adaptive crossover, mutation factor, and Metropolis acceptance criterion are designed to improve the convergence speed. Finally, a feedforward control structure based on identification is designed to compensate for the model deviation. Simulation and experimental results show that the improved differentiator can effectively improve the tracking speed and derivation accuracy of the signals. Compared with other algorithms, the proposed identification method has a faster convergence speed and higher identification accuracy, and feedforward compensation control can effectively correct model parameters and improve control accuracy.