In this paper, a semi-active nonlinear artificial intelligence compound controller for marine engines was developed to improve vibration reduction characteristics across a wide frequency range. A mathematical model was developed and investigated for two-stage vibration isolation systems (Virgin IslandsS) considering vertical, roll, and pitch motion. The passive mathematical model of the magnetorheological damper was also developed and integrated with the two-stage VIS. The passive numerical analysis was validated through the experimental investigation. Force transmitted from the engine to the base was evaluated on the validated model using four different strategies, that is, conventional passive, semi-active low, semi-active high, and semi-active controlled damper. In a semi-active–controlled damper, a mathematical model is developed for controlling the force by developing a nonlinear artificial intelligent compound controller (NAICC) using the algorithm of chaotic fruit fly and fuzzy logic control. The results show that the application of NAICC has a better isolating effect than the passive VIS over a broad spectrum of frequencies. By strengthening the control effect in the low-frequency resonance zone, marine engine vibration reduction performance was significantly enhanced.