The invention discloses a cement concrete pavement notch groove depth three-dimension detecting algorithm and system. The cement concrete pavement notch groove depth three-dimension detecting algorithm and system use a data collecting system based on a line laser and area-array camera, and collected three-dimensional image data are denoted as y. A computer reads the three-dimensional image data matrix y. Bidirectional standard deviation smoothing is carried out on the data matrix y and an image data matrix Q after smoothing is obtained. Morphological smoothing is carried out on the data matrix Q after smoothing and a matrix M' m*n is obtained after smoothing. A height histogram Hist of the three-dimensional data matrix M' m*n is established. A threshold value th of the matrix is evaluated. All data greater than or equal to the threshold value th in the M' m*n are stored in a one-dimensional matrix O1, all data less than the th are stored in a one-dimensional matrix O2, and the denoised pavement three-dimensional data matrix M' m*n is divided into two parts. An arithmetic mean value avg1 of the data in the matrix O1 and an arithmetic mean value avg2 of the data in the matrix O2 are calculated respectively, and then the average depth of a notch groove area is calculated. The cement concrete pavement notch groove depth three-dimension detecting algorithm is good in stability, high in reliability, and small in a relative error compared with a sanding method.