To improve the lift-to-drag ratio of hypersonic vehicles， an important idea is to construct favorable interactions between shock waves and expansion waves forming on different parts of the vehicle. In the existing design methods based on this idea， the geometric parameters are calculated by the shock-wave and expansion-wave relationships of two-dimensional or axisymmetric inviscid flow fields. Due to the influence of three-dimensional effect and viscosity， the high lift-to-drag ratio configurations designed by existing methods shows significant performance degradation compared with ideal design performance. To solve this problem， an optimization design method derived by shock-wave morphology is proposed. This method takes the target shock-wave morphology instead of the aerodynamic performance as the objective to guide the optimization direction of geometric parameters. The method is applied to a three-dimensional wave cancellation biplane where the main wing and the upper wing have favorable interference. The optimized configuration outperforms the initial configuration designed by the two-dimensional inviscid method in terms of both shock-wave morphology and aerodynamic performance， which proves the effectiveness of the proposed optimization design method. Compared with the diamond wing， the wave cancellation biplane has the advantage in the lift-to-drag ratio under the design condition.