A fluorescence hyperspectral microscopy system featuring structured illumination and parallel recording includes a light projection sub-system, a detection sub-system, and an electrical controller. The light projection sub-system includes a digital light processing (DLP) module for generating linear excitation light, a first lens set, an optical path allocation element, and an objective lens. The detection sub-system includes a second lens set, a frequency-dividing reflection element, a two-dimensional light detector, and a light collection element. With the detection sub-system performing detection in conjunction with the light projection sub-system, and the electrical controller controlling the DLP module, a two-dimensional moving platform, and the two-dimensional light detector, the fluorescence hyperspectral microscopy system provides increased resolution and can obtain accurate information in spatial and spectral dimensions and hence a four-dimensional hyperspectral image of the object under detection.