The success of a flapping wing air vehicle flight is strongly related to the flapping motion and wing structure. Various disciplines should be considered for analysis and design of the flapping wing system. A design process for a flapping wing system is defined by using multidisciplinary design optimization. Unsteady aeroelastic analysis is employed as the system analysis. From the results of the aeroelastic analysis, the deformation of the wing is transmitted to the fluid discipline and the dynamic pressure is conveyed to the structural discipline. In the fluid discipline, a kinematic optimization problem is solved to maximize the time-averaged thrust coefficient and the propulsive efficiency simultaneously. In the structural discipline, nonlinear dynamic topology optimization is performed to find the distribution of reinforcement by using the equivalent static loads method for nonlinear static response structural optimization. The defined design process is applied to a flapping wing air vehicle model and the flapping wing air vehicle model is fabricated based on the optimization results.