To solve the misaligned grating problem in the double-pass single-parallel two-grating compressor system, a monitoring system with simple structure is designed. Numerical simulation is investigated based on the system scheme and an original method for online adjusting gratings is proposed. All dimensions of two misaligned gratings are analyzed and then separated to adjust step by step based on the relationship between monitoring variables and misadjustment until the misaligned gratings in the vacuum chamber have been adjusted back to the ideal position. The alignment error and reliability discussion of the method are presented. Based on the existed parameters of the system, the accuracy range from 0.30 μrad to 2.78 μrad is obtained.