Multi-channel three-dimensional measurement based on phase calculation uses multiple optical channels at the same time, which results in the coupling of crosstalk, chromatic aberration, lens distortion and nonlinear response of devices, and affects measurement results and detection accuracy. Aiming at this problem, based on the error types of the collected images, the errors are divided into the light intensity error between the image pixel brightness to the actual brightness and the position deviation of spatial position distribution of image pixels. Then the light intensity error relation and the position deviation relation are constructed respectively and carry on the quantitative measurement to the detection system. Finally, a systematic error compensation method is proposed, which corrects the errors of intensity and pixel position of the collected image by using the established error relation, and compensates the influence of the above errors on the measurement results. The error compensation method proposed in this paper is used in multi-channel three-dimensional measurement of a standard step, the experimental results show that the measurement error can be reduced from 0.678 mm to 0.031 mm, and the method has practical value for the high-precision three-dimensional measurement of such a system.