The invention discloses a system for automatically acupuncturing acupuncture points of rats and mice. The system comprises a rat fixing device, an acupuncturing device, and a computer, wherein the computer controls the acupuncturing device to perform actions, the rat fixing device comprises a rat bed, four-limb rings, a neck ring and a trunk softening belt, the acupuncturing device comprises a telescopic rod, a bracket, a rotation arm, an acupuncturing needle, an acupuncturing needle connection member, a moxa stick box and a pushing device, and the computer comprises a module for controlling the bracket and the rotation arm to move, a module for controlling angles and depth of the insertion needle, a module for controlling the length of a moxa stick which enters the moxa stick box, and a module for controlling the rotation arm to automatically shake. The acupuncturing system can be used for automatically acupuncturing rats and mice, so that labor resources are saved, meanwhile, the danger that operators are bitten by animals when performing acupuncture is avoided, acupuncturing efficiency is improved, and acupuncturing standardization is facilitated; computer software is used to control the acupuncturing device so that a means of intervention on animals is objectively evaluated.