The invention discloses an LED-excited short wavelength infrared fluorescent microscopic imaging system. In the system, laser light emitted by a single-color LED passes through a collimating lens to be collimated firstly and is introduced into a light path of a microscope vertical illumination device, the exciting light is reflected with a dichroic beam combiner and converges onto a back focal plane of a microscopic objective, converging light forms parallel exciting light beams after passing through the objective and illuminates onto a sample, and a fluorescence probe in the sample is excitedto emit fluorescence; and a fluorescence signal passes through the objective, penetrates through the dichroic beam combiner and is finally received by a detection surface of an InGaAs camera to realize photoelectric conversion, and the signal is transmitted to a computer for data processing to obtain an imaged picture or a video. The LED-excited short wavelength infrared fluorescent microscopic imaging system has the remarkable advantages of high signal-to-noise ratio, high magnification, high resolution, capability of real-time imaging, capability of tomography, large penetration depth, small tissue damage and the like.