The invention discloses a vertical rotating fluorescent molecule tomography imaging system. The imaging system comprises a light source excitation device, an optical fiber switching device, a winding reel, a fluorescence excitation device, a fluorescence detection device, a rotating table, an examination table, a horizontal moving table and a computer. The optical fiber switching device and the winding reel solve the problems of electrical connection, optical transmission and data transmission in the rotating process of an imaging platform, and meanwhile two imaging modes can be switched freely; the design of an optical path of a plane mirror is adopted in an imaging part, the rotation radius of the system is reduced, and therefore the system can be simple and compact; reflecting type two-dimensional fluorescent molecule imaging and transmission-type three-dimensional fluorescent molecule tomography imaging of 360 degrees can be achieved at the same time, the two imaging modes are integrated on the same device, and the amount of information capable of being obtained is increased; the light source excitation device, the optical fiber switching device, the fluorescence detection device and the like are designed in a modular mode, and therefore the portability and the universality are good.