The invention belongs to the technical field of medical imaging, and discloses a single-view-angle reflective near-infrared two-region fluorescence dynamic tomography system and method, and the system comprises a fluorescence imaging module, a CT imaging module, a central control module, a data processing module and an auxiliary module. The wide-field excitation light source is used for irradiating an imaging target, the collecting camera and the excitation light source are located on the same side, the imaging speed is greatly increased through reflection type imaging, and real-time fluorescence tomography can be obtained. According to the invention, near-infrared two-region imaging is adopted, so that the image resolution of three-dimensional reconstruction can be improved; a reflective fluorescence tomography technology is utilized, three-dimensional fluorescence tomography reconstruction is carried out only by using single-view-angle reflection fluorescence data, it is hopeful to achieve wide-field excitation to obtain high imaging speed, and real-time fluorescence tomography is obtained; the structure image of the sample is obtained by combining the single-view CT tomography technology of depth reconstruction, and the sample does not need to be rotated any more, so that the system complexity is reduced, and the imaging speed is improved at the same time.