The invention discloses a collimation modulating X-ray generator. The collimation modulating X-ray generator comprises an X-ray source assembly, a high voltage generator, a collimation modulating device and a cooling device. The X-ray source assembly comprises an X-ray tube with a cathode and an anode and a front collimator. The high voltage generator is used for supplying high direct voltages to the position between the cathode and the anode of the X-ray tube to stimulate an X-ray beam, and the high voltage generator is arranged in an extension cavity of a shell of the X-ray tube. The collimation modulating device is rotatably arranged on the outer side of the front collimator and used for modulating the sector X-ray beam into a continuous pencil X-ray beam. The cooling device can be independently arranged on the X-ray tube and used for cooling the anode in the X-ray tube. The X-ray source assembly, the high voltage generator, the collimation modulating device and the heat pipe cooling device are integrated to be of an integral structure. The collimation modulating X-ray generator is compact in structure and conducive to the miniaturization, modularization and high-efficiency design of safety inspection system equipment.