The objective of the present study is to analyze the effects of waves on the propulsive performance and flow field evolution of flexible flapping foil, and then offer a way to take advantage of wave energy. The effects of regular waves on the propulsive performance of a two-dimensional flexible flapping foil, which imitated the motion and deformation process of a fish caudal fin, were numerically studied. Based on computational fluid dynamic theory, the commercial software Fluent was used to solve the Reynolds-averaged Navier–Stokes equations in the computational domain. Several numerical models were employed in the simulations, which included user-defined function (UDF), numerical wave tank (NWT), dynamic mesh, volume of fluid (VOF), post-processing, and analysis of the wake field. The numerical tank was also deep enough, such that the tank bottom had no influence on the surface wave profile. First, the numerical method was validated by comparing it with experimental results of rigid foil, flapping under waves. The effects of three key wave parameters on the propulsive performance of flexible and rigid foils were then investigated; the results show that higher performance can only be obtained when the motion frequency of the foil was equal to its encounter frequency with the wave. With this precondition, foils were able to generate higher thrust force at larger wave amplitudes or smaller wavelengths. Similarly, the percentage of wave energy recovery by foils was higher at smaller wave amplitudes or wavelengths. From a perspective of wake field evolution, increasing foil velocity (relative to water particles of surrounding waves), could improve its propulsive performance. In addition, flexible deformation of foil was beneficial in not only enhancing vortex intensity but also reducing the dissipation of vortices’ energy in the flow field. Therefore, flexible foils were able obtain a better propulsive performance and higher wave energy recovery ability.