The motion of living organisms such as birds, fishes, and insects, has been analyzed for the purpose of the design of MAV(Micro Air Vehicle) and NAV(Nano Air Vehicle). In this research, natural motion was considered to be applied to the determination of the geometry and motion of AUV(Autonomous Underwater Vehicle). The flapping motion of a number of hydrofoil shapes in AUV was studied, and at the same time, the optimization of the hydrofoil shape and flapping motion was executed that allow the highest thrust and efficiency. The harmonic motion of plunging and pitching of NACA 4 digit series models, was used for the numerical analysis. The meta model was made by using the kriging method in Optimization method and the experimental points of 49 were extracted for the OA(Orthogonal array) in DOE(Design of experiments). Parametric study using this experimental points was conducted and the results were applied to MGA(Micro Genetic Algorithm). The flow simulation model was validated to be an appropriate tool by comparing with experimental data and the optimized shape and motion of AUV was turned out to produce highest thrust and efficiency.