In the fields of earth observation, deep space detection, laser communication, and directional energy weapon, the target needs to be observed and pointed at accurately. Acquisition, tracking, and pointing (ATP) systems are usu-ally designed to stabilize the line of sight (LOS) within sub-micro radian levels. In the case of an ATP system mounted on a mobile platform, angular disturbances experienced by the mobile platform will seriously affect the LOS. To overcome the problem that the sampling frequency of detectors is usually limited and achieving sev-eral hundreds of hertz is difficult, the wide-bandwidth inertial reference system (WBIRS) and fast steering mirror are usually integrated into ATP systems to mitigate these angular disturbances. To reduce the structural stress, a flexible support providing two rotational degrees of freedom is usually adopted for the system. However, the oc-currence of resonant points within the bandwidth will be inevitable. Measurements have to be taken to compen-sate these low-frequency resonant points to realize a wide bandwidth and high precision. In this paper, the low-frequency resonant points of a system were simulated using finite element analysis and tested by a system iden-tification method. The results show that the first-order resonance happened at 34.5 Hz with a gain of 28 dB. An improved double-T notch filter was designed and applied in a real-time system to suppress the resonance at 34.5 Hz. The experimental results show that the resonance was significantly suppressed. In particular, the reso-nance peak was reduced by 79.37%. In addition, the closed-loop system settling time was reduced by 36.2%.