As the precision of advanced semiconductor equipment continues to improve, the impact of environmental vibration on precision equipment is increasing. Active vibration isolation technology is widely used in precision equipment to effectively isolate low-frequency vibration. In order to further improve the vibration isolation effect, the control bandwidth of the active vibration isolation system is gradually increased, and the limitation of flexible modes on the overall performance of the system is gradually reflected. In engineering, the resonance peaks caused by flexible modes are usually suppressed by second-order notch filters. Faced with the phenomenon of multiple flexible resonant peaks superimposed in the actual system, the traditional filter design faces the problems of complex parameters, long time consuming, poor suppression effect and large phase loss, etc. In this paper, the second-order notch filter is used to suppress the resonant peaks caused by flexible modes. Meanwhile, based on the amplitude-frequency characteristics of the second-order notch filter, a new parametric design method is adopted, which is simple and time-consuming. The proposed notch filter can accurately suppress the flexible resonance peaks while causing less phase loss, which is conducive to realizing a larger system bandwidth and thus improving the control effect.