In this paper, an innovative approach is proposed to mitigate ship engine vibrations by integrating a semi-active control system with magnetorheological (MR) dampers and an Adaptive Neuro-Fuzzy Control System (ANFIS). The ANFIS controller adjusts MR damper damping force to effectively adapt to engine vibrations. A comprehensive mathematical model simulates the complex dynamics of the ship engine vibration system, validated with real-world data. The model incorporates engine vibration measurements and MR damper properties to train the ANFIS controller. Compared to passive control systems, the proposed semi-active system reduces torsional vibrations by 22.606% and longitudinal vibrations by 29.840%. The ANFIS controller dynamically adjusts damping force in response to engine conditions, ensuring optimal performance. This system effectively mitigates ship engine vibrations, improving overall ship performance and passenger comfort. Consistency between modeling and experimental results confirms the system's viability and efficacy.