The invention discloses a spatial consistency correcting method of a multi-spectral imaging system. The method comprises the following steps: measuring response values of a series of gray paper at different positions of the objective table of the multi-spectral imaging system, meanwhile, measuring a color block response value used for reflectivity reconstruction in the multi-spectral imaging system, and by means of a polynomial regression model, mapping the response values of the different gray paper at different positions to the response values of the central position by using the position information as independent variables, and meanwhile, mapping the response values of the color block used for reflectivity reconstruction to the target value by taking the position information as an independent variable. The spatial consistency precision requirement and the reflectivity reconstruction precision requirement in the multi-spectral imaging system are met at the same time, so that after spatial consistency correction is carried out, the spatial consistency chromatic aberration of the system is greatly reduced, and meanwhile, the chromatic aberration mean value of the reflectivity reconstruction is also reduced.