Employing flexible hydrofoil profiles is an efficient methodology for implementing flow control and enhancing energy harvesting for the flapping-foil system. In this study, a two-dimensional numerical model was established based on the commercial computational fluid dynamics platform ANSYS-Fluent® 16.0 and validated using experimental data to investigate the flexible hydrofoil under the semi-passive coupled-pitching mode. The effects of the deforming segment, related parameters, and phase angles on the hydrodynamic characteristics and power output performance were studied. Evidently, an adequately deformed hydrofoil profile has a positive influence on the flow structures to enhance the pressure difference on the hydrofoil surfaces and hydrodynamic torques leading to improved performance. Compared to the leading-segment part (LSP), the deformation of the trailing-segment part (TSP) better enhanced the power output in the semi-passive system. Because the trailing segment covered all elements from the pivot to the trailing edge, the peak values of the cycle-averaged efficiency and power coefficient were 51.4% and 0.99 as the TSP deforming coefficient was 6.3 and the phase angle was 90°, which is higher than those for the rigid hydrofoil by 35.2% and 61.5%, respectively.