The invention discloses a functional hyperspectral CT (computed tomography) imaging-based substance recognition method and a functional hyperspectral CT imaging-based substance recognition system. The system comprises an X-ray tube, a photon counting detector, a two-dimensional translation platform, a rotating platform, a three-dimensional motion controller and a control center, wherein the X-ray tube is connected with a high voltage generator to emit an X ray to scan a tested sample; the rotating platform is positioned in front of the emitting end of the X-ray tube to support the tested sample; the photon counting detector is positioned on the two-dimensional translation platform to acquire hyperspectral data; the three-dimensional motion controller is connected with the rotating platform to control the rotating platform to rotate, and is connected with the two-dimensional translation platform to control the two-dimensional translation platform to translate; the control center is connected with the three-dimensional motion controller, the photon counting detector and the high voltage generator to control the three-dimensional motion controller and the high voltage generator, receive the hyperspectral data and recognize the tested sample. The method and the system have a broad application prospect in disease diagnosis, food safety and nondestructive testing.