With the continuous development of power transmission technology and automation control technology, the application of high-power inverter devices in modern ship power systems is increasing. Moreover, as the ship operates under different conditions such as cruising and platform lifting, the degree of harmonic pollution in the ship’s electrical grid varies. If harmonics in typical operating conditions like cruising and platform lifting are not effectively managed, it can seriously affect the safe operation of the ship. To address this issue, this paper proposes an intelligent harmonic suppression method for active power filters based on fuzzy PID and model predictive control. It combines fuzzy control with conventional PID control to enhance control robustness. The optimization objective in the model predictive current control is shifted from compensation current provided by the active power filter to the inverter output voltage. By adjusting the phase of the inverter output voltage corresponding to the voltage vector reference value, the range of inverter output voltage vectors participating in rolling optimization is narrowed, thereby achieving control of harmonic currents. Finally, by modeling the ship’s integrated power system and simulating two operating conditions, cruising and platform lifting, this study analyzes voltage waveforms and harmonic content before and after harmonic suppression using fuzzy PID and model predictive control active power filters. The results demonstrate that the proposed method can significantly improve voltage quality in power systems under power supply voltage distortion and has excellent harmonic suppression effects.