The inertial reference unit based visual axis stabilization is a main technique used to overcome external disturbance of the moving carrier photoelectric tracking system and realize micro-radian or even sub-micro-radian level tracking. The initial calibration of inertial reference unit requires the construction of a closed-loop control loop with the eddy current displacement sensor as the angular position feedback element. The angular position control accuracy is the main factor that affects the pointing accuracy of the photoelectric tracking system. To solve the problems such as base disturbance and sensor noise faced by inertial reference unit system position control, the varying gain PI control method based on frequency band estimation is proposed. The improved disturbance observer is designed to reduce the influence of middle and low frequency sensing noise on the control accuracy, and the frequency band estimator is designed to realize the subdivision of external disturbance frequency band and dynamically adjust the controller gain accordingly. Simulation and experimental results show that the VGPI-IDOB control algorithm can effectively improve the position control accuracy of the system. Under the condition of no input, the static output root mean square of the system is reduced by 67. 3% compared with that of the PI controller. Under the influence of 15 Hz, 1 mrad sinusoidal input, 20 Hz, 0. 097 mrad disturbance, the position control accuracy of VGPI-IDOB is improved by 72% compared with the PI structure.