Addressing the challenges of low efficiency and instability in the passive energy extraction of wave-powered boat under wave conditions, a fluid-multibody coupled non-holonomic constraint model for an active control hydrofoil system is developed. The motion response and propulsion performance of the active propulsion mode are thoroughly investigated. The optimal propulsion interval of the hydrofoil under various wave conditions is analyzed through numerical simulation, and the optimization of the active control model on the energy harvesting of the hydrofoil propulsion mechanism is demonstrated by combining with the flume experiments. The results demonstrate that the active control model effectively enhances the flow structure generated by the hydrofoil, increasing surface pressure differences and stabilizing the wake vortex, which together improve the propulsive performance of the wave-powered boat. Additionally, a symmetrical pitch cycle of the hydrofoil proves to be more efficient in boosting power output, while torque input optimized via simulation data delivers greater propulsive force.