Disclosed is a dual-energy ray imaging method and system. The method comprises: calculating the mass thicknesses of the materials in the overlapped area of two materials by using a calibrated surface fitting method, and then decomposing a pair of original high-energy and low-energy data for this pixel into two high-low-energy data sets corresponding to the two materials, and finally calculating and acquiring the composition result of different materials for each pixel. The disclosure is especially advantageous in that the problem of error recognition of materials due to the two overlapped materials can be eliminated and the stratified imaging of multiple materials can be achieved, thereby improving the accuracy of the substance recognition and reducing the rate of false positive and false negative which is very important to the applications in the field of security check and anti-smuggling.