Abstract: Flapping wings harvest kinetic energy from fluids by utilizing the coupled heave and pitch motions of an airfoil. Considerable research has been conducted on the energy-harvesting motion of flapping wings, primarily focusing on experimental and simulation studies that examine how the geometric and kinematic parameters affect the energy utilization efficiency. However, analyses of the flow structures and flow characteristics during the energy-harvesting process of flapping wings are relatively scarce. This study employs the proper orthogonal decomposition (POD) and dynamic mode decomposition (DMD) methods to thoroughly analyze the flow field in flapping wing energy harvesting. The primary focus is a comparative analysis of the wake flow characteristics between the original flapping wing and that equipped with leading- and trailing-edge flaps during their heaving and pitching motions. Through this comparison, the differences in flow structures and energy distributions between the flapping wing energy harvester with and without the control method are revealed, providing a theoretical basis for the development of more efficient energy capturing methods. The results demonstrate that lower-order POD modes can capture the main energy structures in the flow field, while the DMD method can effectively identify the frequency characteristics and the stability of unsteady structures. The application of active control to the flapping wings significantly improves their flow characteristics, reduces detrimental multi-frequency structures, and thereby optimizes the flow field and enhances the energy harvesting efficiency of the flapping wings.