To address the issue of occupant vibration comfort in vehicles under complex road conditions, this study establishes a vibration control system for a magnetorheological (MR) seat coupled with a four-degree-of-freedom human model and performs dynamic analysis. Through the transfer matrix method for multibody systems, the dynamic model and the corresponding topology of the MR seat-occupant system are established and occupant vibration response is obtained. Numerical simulation and comparative analysis reveal that the MR semi-active seat reduces the RMS values of acceleration for key human body parts (head and neck, upper trunk, viscera, and lower trunk) by the average of 25.5%–30.4% and the peak values by 9.8%–32.6%. Notably, the most substantial vibration reduction occurs in the regions of viscera and lower trunk, with RMS values decreased by up to 39.0%. Compared to a conventional passive system, the MR seat demonstrates superior vibration isolation performance in the low-frequency range based on acceleration frequency response characteristics. It effectively attenuates amplitudes within the occupant’s physiologically sensitive frequency bands, leading to the significant enhancement of ride comfort and ride quality.