The invention provides an automatic identification method and system of a pavement disease image. The method comprises: a shot pavement image is preprocessed, wherein preprocessing includes Gamma gray scale correction, Gaussian filter enhancement and local adaptive binarization; edge detection is carried out on a binarized image; connected domain contour detection is carried out on the image after edge detection to obtain the number of the connected domains and external rectangles of connected domain contours; according to the shapes of the external rectangles of the connected domain contours, a region of a pavement crack is determined; on the basis of position information of the region of the pavement crack, a crack region image is extracted from the image after edge detection and a black template is superposed to form a crack feature image with the size identical with that of the original image; and on the basis of a convolution neural network, the crack feature image is classified. Compared with the prior art, the method and system have the following advantages: the detection efficiency of crack positioning in the pavement disease is high; and for crack images with different features, robustness is high.