Vibrations generated from equipment mounted on ships radiate into the water and affect covert operation capabilities. Accordingly, various studies are being conducted to reduce vibration transmitted from mounted equipment. In this study, a system consisting of mounting equipment, a 3-axis active mount, a middle pedestal, and a lower mount of the middle pedestal was modeled using a finite element analysis program, and a mobility model was constructed by calculating the frequency response function between the positions required for analysis. The error signal (primary path) obtained using the mobility model and the response at the operating point by the control force of the actuator (secondary path) are applied to the narrowband Fx-LMS algorithm for vibration control, and the control performance was compared. Through coupling analysis of the middle pedestal, the control influence according to the rigidity of the middle pedestal was analyzed. As a result of the control simulation, the time required for vibration control was controlled approximately 6 times faster in the model, with increased stiffness of the middle pedestal, and the vibration reduction performance was predicted to improve by a minimum of 0.9 dB and a maximum of 13.3 dB. Through this study, a simulation model that can provide a guide for the design of the middle pedestal of a ship was obtained, and it is expected that it can be utilized for a preliminary design review before manufacturing the middle pedestal of a ship.