The laser seeker testing system is a special testing equipment for the parameter calibration and performance testing of the laser seeker. Its performance and precision determine the quality of the seeker. In order to improve the performance of a laser seeker testing system and restrain the influence of time-varying periodic disturbance on the testing system, an iterative learning control method based on spatial domain was proposed. By analyzing the time-domain and position-domain spectrum of the disturbance components at different velocities, it was obtained that periods of the disturbances were time-varying but position-fixed. Based on the idea of iterative learning, an iterative learning control structure of the spatial domain was carried out. According to the convergence condition of the algorithm and the phase delay characteristic of the filter, the control parameter principles were derived and the phase compensation methods were demonstrated. Its application effect was verified by experiments. The experiment under the command of maximum rotation speed shows that the steady-state tracking error of angular position is decreased by 65.8%, and further, the corrected steady-state tracking error of angular position is decreased by 61.5% after adopting the iterative learning control method of spatial domain.