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A bi-objective optimization problem for flapping airfoils is solved to maximize the time-averaged thrust coefficient and the propulsive efficiency. Design variables include the plunging amplitude, the pitching amplitude and the phase shift angle. A well defined Kriging model is used to substitute the time-consuming high fidelity model, and a multi-objective genetic algorithm is employed as the search algorithm. The optimization results show that the propulsive efficiency can be improved by reducing the plunging amplitude and the phase shift angle in a proper way. The results of global sensitivity analysis using the Sobol’ s method show that both of the time-averaged thrust coefficient and the propulsive efficiency are most sensitive to the plunging amplitude, and second most sensitive to the pitching amplitude. It is also observed that the phase shift angle has an un-negligible influence on the propulsive efficiency, and has little effect on the time-averaged thrust coefficient.