In order to suppress the time-varying disturbance in the tip-tilt correction system, an adaptive disturbance suppression method based on characteristic disturbance frequency identification is proposed in this paper. The least mean square error criterion is used to identify the characteristic disturbance frequency of the closed-loop system error, and the identified filtering parameters and controller adjustment are designed in parallel. At the same time, a method based on frequency splitting is proposed: combining low-frequency disturbance with high-frequency disturbance suppression, which further improves the speed of characteristic frequency identification and simplifies the design process, and realizes adaptive disturbance suppression in the closed-loop bandwidth. The closed-loop verification of the proposed method is carried out in the tip-tilt correction device. The experimental results show that the method can quickly identify the characteristic disturbance and adaptively adjust the controller, which can improve the closed-loop performance of the system under single-frequency and multi-frequency time-varying disturbance.