The invention relates to a method and system for rapidly three-dimensionally microimaging a large sample. The method comprises the following steps: 1, a sample is embedded in a sample block and is fixed on a precise three-dimensional electric translation platform; 2, a digital micro mirror array works in a binary modulation mode, and is used for carrying out binary modulation on illuminating light to form structure striations, a structured light microscope collects an image of the surface layer of the sample within a depth of 1-100micrometers; 3, completing the imaging of the inner surface layer of an imaging region, removing an imaged part of the surface layer of the sample block by using a diamond or hard alloy tool; and 4, repeating the steps 2 and 3 until a data acquiring task is completed. According to the invention, the digital micro mirror array works in the binary modulation mode, the imaging speed is effectively increased; and with an exposure synchronization method of the digital micro mirror array and a surface array camera, the sample can be irradiated by exciting light only when a surface array camera is exposed, the exposure quantity of the sample is further reduced, and the negative effects of a light bleaching effect to imaging is avoided.