A tomographic imaging method which includes the steps of activating fluorescence in a surface layer of a protein-marked or fluorescent dye-marked biological tissue sample not emitting fluorescence or only emitting specific fluorescence to acquire an activated surface of biological tissue sample; performing fluorescence excitation on the acquired surface biological tissue sample, and imaging the fluorescence to acquire a fluorescence image of the surface layer; cutting off the surface layer; exposing an inactivated new surface layer after cutting the surface layer; repeatedly performing activating, imaging and cutting off steps for the new surface layer to repeat tomographic imaging in such a manner till acquiring a two-dimensional image of each layer of the biological tissue sample; and overlapping the two-dimensional images to acquire a complete three-dimensional image of the biological tissue sample, thus acquiring three-dimensional structure information of the entire sample.