Pseudo dual-energy material identification systems and methods with under-sampling are disclosed. The system comprises a ray generating device (11), a mechanic rotation control section (12), a data collecting subsystem (13) comprising a first tier of detectors and a second tier of detectors, and a master control and data processing computer (14). The system utilizes a CT-imaging-based material identification method with under-sampled dual-energy projection data, in which only a few detectors at the second tier are used to perform dual-energy projection data sampling, and optimization is made on the procedure of solving an equation system.