The present invention provides a method and system of material identification using binocular steroscopic and multi-energy transmission image. With the method, any obstacle that dominates the ray absorption can be peeled off from the objects that overlap in the direction of a ray beam. The object that is unobvious due to a relatively small amount of ray absorption will thus stand out, and the material property of the object, such as organic, mixture, metal and the like can be identified. This method lays a fundament for automatic identification of harmful objects, such as explosive, drugs, etc., concealed in a freight container.