Abstract The aerodynamic performance of flexible flapping wing is investigated through numerical simulation based on fluid-structure coupling method, which is developed on the Navier-Stokes equations and structural dynamic equations. The interface data exchange method is based on radial basis function and the moving mesh generation method is based on infinite interpolation. The flexible flapping wings we investigated are constructed of a carbon fiber skeleton and a thin extensible membrane in a bird like scale with the chord Re of 5e4. This research focused on the influence of different flexibilities with same wing structure topology. The flexibility is controlled by diameters of carbon fiber skeleton and five structures are analyzed. The simulation results proved that the structural deformation has a significant effect on the aerodynamic force, especially on the thrust. A wing with maximum rigidity has the best lift performance but the worst thrust performance, and vice versa. A wing with medium rigidity gets better performance in both lift and thrust. According to the results, it is necessary to balance the relations between structure flexibility and aerodynamic performance. Meantime, the characteristics of different structures are consistent with the variety of attack angle and flapping frequency.