The invention provides a surgery mechanical arm stroke correcting system and method. The system comprises a surgery mechanical arm, a fluoroscopy device, a processing device, a control device and a target marking structure; the target marking structure comprises at least four C calibration bodies, wherein the four C calibration bodies are not located on the same plane; the control device controlsthe surgery mechanical arm to move according to the theoretical stroke so as to drive a surgical tool on the surgery mechanical arm to move towards the planned path of the target marking structure; the fluoroscopy device photographs the target marking structure and the surgical tool controlled to be moved according to the theoretical stroke, and the photographed images are transmitted to the processing device; the processing device determines the actual position of the surgical tool and the offset of the planned path according to the position relation of the target marking structure and the surgical tool in the photographed images; the offset is used for correcting the theoretical stroke. According to the surgery mechanical arm stroke correcting system and method, the stroke of the surgerymechanical arm can be corrected, and positioning errors are reduced.