To address parallelism error compensation in a dual-rotation multi-channel double crystal monochromator (DCM), we propose a method using an autocollimator to measure the quasi-static parallelism of diffraction surfaces and an S-curve trajectory planning method. First, we analyze the structure and motion of the monochromator. Then, we present a measurement system framework using the autocollimator. We also propose an S-curve trajectory planning algorithm to optimize the motion trajectory based on parallelism measurements. Finally, experiments on the constructed platform show that the measurement system achieves a 0.5" resolution, with crystal angle transitions varying by hundreds of arcseconds. The S-curve planning algorithm reduces trajectory tracking error by 58.7% and 63.9% compared to a 5th order polynomial and unplanned trajectories, respectively, with a 6.1" tracking error. These results confirm the method's efficacy in enhancing the performance of the monochromator.