The harmonic signal generated by power equipment on naval vessels is a typical narrowband interference, which seriously affects the stealth performance of naval vessels. The float raft active vibration isolation system is characterized by strong adaptability and good controllability, which can effectively isolate low-frequency interference. For the active vibration isolation system, the control strategy is one of the core, and the precise mathematical model is difficult to be established. The fuzzy control does not rely on the precise mathematical model of the controlled system, which cannot only provide an intelligent path for the active control of the complex floating raft system, but also effectively suppresses the narrowband interference caused by naval vessels' power equipment. Therefore, depending on the existing float raft active vibration isolation platform, this paper outlines a design for a two-input/single-output optimized fuzzy control system based on vibration acceleration, variation of vibration acceleration and control voltage. In an optimized fuzzy control system, an algorithm of quantum behavior particle swarm optimization algorithm (QPSO) is proposed to optimize quantization factor and scale factor because quantization factor and scale factor are set subjectively with strong subjectivity and blindness, and the stability of the control system is roughly verified. Therefore, simulations and experiments are carried out to test and verify the performance of control system designs outlined in this paper. Through comparative analysis, it shows that the floating raft active vibration isolation system with a fuzzy control system based on the QPSO algorithm has a favorable effect on low-frequency narrowband interference.