The invention discloses a microscopical hyperspectral chromatography three-dimensional imaging device, which comprises a light source unit, a three-dimensional scanning platform, a front microscopical light path unit, a beam-splitting imaging unit, a signal pretreatment unit, a signal acquisition unit and a control unit. The device integrates a hyperspectral imaging technology, a microtechnique, a fluorescence molecular tomography and a three-dimensional imaging technology. The device can obtain the two-dimensional hyperspectral chromatography images under conditions of multiple wavelengths and angles of an object and can obtain the light spectrum under wavelength corresponding to each pixel; meanwhile, based on a three-dimensional image reconstruction technology, the device can obtain the three-dimensional microscopical hyperspectral image of the object; and combining with the microtechnique, the device can obtain the micro three-dimensional hyperspectral chromatography images of the surface and internal structures of micro objects. Compared with other spectrographs, the device has the advantages of more information, higher precision, more powerful functions and higher stability. The device is suitable for biomedical test, food safety test and ecological environment monitoring.