The harmonic balance method is an efficient frequency-domain approach for computing periodically unsteady flows. Applying harmonic balance method to the rapid calculation of forced periodic motions, an efficient prediction method for dynamic derivatives is established based on the Etkin unsteady aerodynamic model. The method is firstly validated by a standard model of the hypersonic missile hyper ballistic shape, and the harmonic balance method results show great consistency with both time-domain results and experimental data, consolidating the efficiency of our numerical algorithm. The method is subsequently applied for an air-breathing hypersonic vehicle to investigate the capability of the harmonic balance method in modeling unsteady flows around complex geometric configurations. Comparisons with the results of the time-domain method demonstrate that the harmonic balance method is capable of resolving such complicated flowfield with both accuracy and efficiency. To be specific, for the air-breathing hypersonic vehicle, the maximum difference of the dynamic derivatives calculated by the harmonic balance method and the time-domain method is only 6.56%, and the harmonic balance method shows at least an order of magnitude efficiency over the general time-domain method in the current study.