The present disclosure discloses a ray transmission and fluorescence CT imaging system and method. The system comprises: a ray source configured to emit a beam of rays; a rotational scanning device configured to perform rotational CT scanning on an object to be inspected; a transmission CT detector configured to receive the beam of rays which has passed through the object; a fluorescence CT detector configured to receive fluorescent photons excited by irradiation of the beam of rays on the object; a data acquisition unit configured to acquire a transmission data signal and a fluorescence data signal respectively; and a control and data processing unit configured to control the ray source to emit the beam of rays, control the rotational scanning device to perform the rotational CT scanning, and obtain a transmission CT image and a fluorescence CT image simultaneously based on the transmission data signal and the fluorescence data signal.