The invention discloses a cone-beam X-ray luminescence tomography system of combination imaging and a method thereof. The system comprises a charge-coupled device (CCD) camera, an X-ray source, an X-ray detector, an electronic control rotating table and a narrow-band filter, wherein the CCD camera, the X-ray source, the X-ray detector, the electronic control rotating table and the narrow-band filter are coupled with a lens. The CCD camera and the narrow-band filter are fixed in the same direction, and then a to-be-imaged object, the CCD camera and the narrow-band filter are located on the same straight line; the X-ray source and the X-ray detector are placed in the direction perpendicular to the CCD camera, and then the X-ray source, the to-be-imaged object and the X-ray detector are located on the same straight line; and the CCD camera, the electronic control rotating table, the X-ray source and the X-ray detector are controlled to operate by using a computer. According to the cone-beam X-ray luminescence tomography system of the combination imaging and the method thereof, use ratios of X-rays are improved, and medicine of the to-be-imaged object can be fully excited; X-ray irradiation time is shortened, X-ray irradiation doses are reduced, and popularization and application of X-ray excitation imaging are benefited; information fusion of two types of imaging modals is achieved, and more biological characteristics of the to-be-imaged object are acquired.