With the help of the unsteady Etkin aerodynamic model, the harmonic balance method to calculate the dynamic derivatives of complicated configuration was applied. The dynamic derivatives solved by harmonic balance method agree well with the results of time domain method and experimental data, which verified the correctness of codes and the reliability of the harmonic balance method. The harmonic balance method was applied to compute the dynamic derivatives of X-51 hypersonic airframe/propulsion integrative vehicle namely WR-A. A comparison was made with the time domain method to verify the ability of the harmonic balance method for the numerical simulation of unsteady flows around the complicated model and the ability of the computing dynamic derivatives. Results show that even for the vehicle WR-A of the complex configuration, the harmonic balance method was computationally accurate and efficient.