The stern flap is a practical hull appendage equipment that enhances ship navigation performance and saves energy. The existing studies mainly focus on the fixed stern flap, other than an actively controlled one, so it is worth further exploring its effect and mechanism. By implanting the PID controller to the stern flap, this paper proposed a free-running CFD model on the ONRT (the Office of Naval Research Tumblehome) ship coupled with the active-controlled stern flap to investigate the hydrodynamic performance in resonance waves. The free-running performance in calm water and regular waves is numerically researched and verified versus the experimental and referenced results. Then, the effect of different PID coefficients and control strategies of the stern flap on the traveling speed, attitudes, and propulsion performance under the resonance wave condition is conducted, and the influence mechanism is explored. The results show that adopting a fixed flap controller and PID controller can reduce the original speed loss by 4.2% and 6.9%, respectively, and increase the average propulsive efficiency of the propeller by 1.0% and 1.4%, respectively. Further analysis reveals that the global effect of the suppressed motion attitudes due to the installation of the fixed flap effectively contributes to the resistance reduction. However, the local effect of the stern flap increases the resistance due to interaction with the propeller and stern. The PID-controlled stern flap exhibits similar average attitudes compared to the fixed one, which means the resistance reduction of the global effect is kept the same, and the active stern flap further improves the stern flow field, where the resistance increment of the local effect is weakened, enhancing the traveling speed and improving the propulsion efficiency.