This paper meticulously examines the magneto-rheological (MR) damper to exploring its application in a semi-active isolator system. The MR damper’s distinctive capability to regulate damping force through an externally applied magnetic field is investigated via extensive experimental testing. Sinusoidal displacement inputs with varying electromagnet currents reveal a direct correlation between higher current levels and augmented MR damper forces. Validation of the experimental results is achieved through the Viscous Plus Dahl Model, showcasing its accuracy in capturing the damper’s hysteresis behavior. The study extends its scope to practical implementation by integrating the MR damper into a marine diesel engine system. A fuzzy logic-based self-tuning PID controller collaborates with the MR damper to establish a semi-active vibration isolator. The integrated model, encompassing primary and secondary masses, the engine, and the isolator with passive and semi-active systems, is rigorously analyzed. Experimental validation and theoretical simulations, aligned with data gathered from experiments, affirm the model’s fidelity in representing the MR damper. Simulation outcomes underscore the significant enhancement in vibration reduction characteristics of the semi-active isolator system compared to its passive counterpart, particularly evident in the improved performance of the 1200 kg engine under diverse operating conditions.