Disclosed is a method for automatic classification of pathological images based on a staining intensity matrix. This method directly extracts the staining intensity matrix irrelevant to a stain ratio, a staining platform, a scanning platform and some human factors in the pathological image as the feature information of classification, without restoring normalized stained images, while retaining all impurity-free information related to diagnosis. It avoids the phenomenon that the diagnostic effect of the existing computer-aided diagnosis method of pathological images based on the traditional color normalization method changes with the changes of the selected standard pathological sections. Moreover, it avoids the error introduced by the need to restore the stained image, and has a higher diagnostic accuracy and a more stable diagnostic effect. At the same time, the method can realize the diagnosis of pathological images in a shorter time, which is easy to realize and more practical.