The invention discloses an automatically radiation-proof FMT-and-CT dual-mode imaging system. The automatically radiation-proof FMT-and-CT dual-mode imaging system comprises a signal collecting module, a controller module, a data transmission module, a power module and an automatically radiation-proof module, wherein the signal collecting module is used for collecting fluorescence excitation imaging data and X-ray computerized tomography data of an imaging sample, the controller module is used for controlling operation, parameter setting, data processing and data storage of other modules, the data transmission module is used for transmitting internal data of the system, the power module is used for providing electricity for the whole system, and the automatically radiation-proof module is used for protecting a CCD camera and reducing damage caused by X-rays to the CCD camera. The automatically radiation-proof FMT-and-CT dual-mode imaging system can achieve dual-mode rapid imaging of FMT and CT, and due to the fact that the automatically radiation-proof module is designed, when an X-ray power source is turned on, the CCD camera is effectively protected, and damage to an internal sensitization chip can be reduced.