The purpose of this paper is to investigate the vibration phenomenon occurring in the structure such as a ship with the hemispherical substructure and operating at fixed frequency, and to suggest the active vibration control method using the Fx-LMS algorithm to reduce vibration amplification. In order to study the possibility of reducing vibration in the hemispherical structure, the active vibration control model was developed and a vibration control experimental device for the hemispherical structure was constructed. The narrowband Fx-LMS algorithm was developed to enable precise real-time control at a specific frequency, and the secondary path for dynamic control was modeled with two coefficients per frequency. The experimental device is equipped with three exciters, six 3-axis actuators, and six 3-axis error sensors, which can acquire 18 error sensor signals. Real-time secondary path tracking was possible with the secondary path consisting of two coefficients and the control algorithm, and effective vibration control performance was confirmed through this. And the experimental results of active vibration control of the exciter for three frequencies showed that the exciter vibration was reduced by a minimum of 63.7% and a maximum of 97.7%, which shows the possibility of reducing the vibration of the structure in real time using the proposed method.