As a core component of the X-ray absorption fine structure spectroscopy (XAFS) system, the multi-channel double-crystal monochromator (DCM) can improve the time resolution of the system significantly. In contrast to the conventional single-channel DCM, the multi-channel DCM includes more pairs of crystals that are located separately in the master and slave motor axis with the same driving direction. However, a mismatched parallelism in the pitch direction, which can result from the manual mounting operation between the two separated crystals, directly affects the performance of the flux and the angular stability of the monochromatic beam. This poses a significant challenge to the precision position tracking of this system. In this paper, the mounting errors were translated into repetitive errors in the slave motor when the master motor was rotated at a constant velocity. Therefore, the iterative learning control (ILC) was considered in order to improve the tracking accuracy of the slave motor motion. The zero-magnitude error controller (ZMETC) was used to calculate the learning function to accelerate the convergence of the control inputs, and the convergence conditions of the control signal and error were also given. To validate the effectiveness of the proposed method, comparative experiments were performed on the motor motion platform. Experimental results indicated that the ILC effectively decreased the parallelism errors of the multi-channel DCM under various trajectories by comparing them with feedback controllers and the ZMETC, respectively.