The invention relates to an indwellable fluorescence microscopy endoscopic imaging system, which belongs to the technical field of fluorescence microscopy. An intervention and indwelling part is a self-focusing lens which is inserted in a micro-wound of a live animal; an excitation light and fluorescence transfer part is formed by sequentially connecting an optical fiber connecting device, an image transmission optical fiber bundle and an optical fiber bundle fixing device, and the front end surface of the image transmission optical fiber bundle and an observed region in a tissue are conjugated relative to the self-focusing lens; a fluorescence photography part consists of a microscope objective, a dichroic mirror, a fluorescence filter and a CCD device which are horizontally arranged along a fluorescence emission main shaft, and the CCD device and the back end surface of the image transmission optical fiber bundle are conjugated relative to the microscope objective; and an excitationlight generation part is formed by sequentially connecting a light source, an excitation light filter and a lens group, and an excitation light main shaft and the fluorescence emission main shaft areorthogonal and both form an angle of 45 degrees with the dichroic mirror. The invention has the advantages of easy realization of high-speed video capture for observing dynamic change of a fluorescent labeled target and carrying out continuous observation of the same position of the live animal for on a long-term basis.