A dual-energy material identification method and system with under-sampling is disclosed. A CT image of the object is obtained by using the CT image reconstruction method, while the dual-energy projections are under-sampled to obtain a few samples. Photoelectric coefficient integral and Compton coefficient integral are computed from these dual-energy projection data. The CT image is segmented into regions with image processing technique, and the regions are labeled. The length by which a few dual-energy rays crosses each labeled region is computed, and an equation system is established with dual-energy preprocessing dual-effect decomposition reconstruction method to compute Photoelectric coefficient and Compton coefficient, and then atomic number and electron density of material in each region are computed. The material of the object can be identified with the atomic number.