The invention relates to the field of small animal imaging, solves the problems that in the prior art, the image resolution is low and the image acquisition time is long, provides a photon counting-type dynamic diffusion fluorescence tomography system which has high sensitivity and image resolution and achieves the purpose of dynamic diffusion fluorescence tomography with short measurement time. In order to achieve the purpose, the invention adopts the technical scheme as follows: the photon counting-type dynamic diffusion fluorescence tomography device comprises a light source system used for fluorescence excitation, an imaging chamber system used for fixing and moving a detected object, a light switch used for switching a detection passage, a light-filtering system used for filtering off excited light signals, a detection system used for detecting light signals, and a computer used for integrated control of an attenuator, the light switch, a motor-driven light filtering wheel, a photomultipler tube and a photon counting module as well as image reconstruction. The invention is mainly applied to small animal imaging.