The invention discloses a fluorescence detector. The fluorescence detector comprises a laser beam combining module, a confocal scanning module, a spectral imaging module, a fluorescence microscope and a control display module. The laser beam combining module comprises two near-infrared light continuous lasers, a laser collimating lens, a reflecting mirror and a beam combining lens. The confocal scanning module comprises three switchable dichroic mirrors, three optical filters, a scanning galvanometer, a scanning lens, a pinhole lens and pinholes. The spectral imaging module comprises a beam splitter prism, a focus lens, three slits and three photomultipliers. The fluorescence microscope comprises a total reflection prism, a barrel lens, a micro-objective, a nanometer displacement platform and a sample platform. The control display module is used for controlling the laser, the scanning galvanometer, the micro-objective and the nanometer displacement platform and displaying the image. The fluorescence detector is capable of overcoming the disadvantage of low detection depth of the prior art, realizing the centimeter-level fluorescence detection and simultaneously realizing the fluorescence positioning and component analysis, and the fluorescence detector has broad application prospect in in-vivo fluorescence detection field.