The invention relates to an artificial intelligence-based anatomical variation recognition prompting method and system, and the method comprises the steps: collecting an endoscope image in real time, and obtaining real-time organ segmentation data and instrument key point data according to an endoscope organ segmentation model and an instrument key point detection model; acquiring a position relationship between the variation structure and the surrounding organs by analyzing the preoperative iconography image, extracting the tissue segmentation data of the surrounding organs of the variation structure of the iconography image for comparison, and judging the position of the variation structure; detecting the position information of the key points of the instrument and the variation structure in real time, prompting the variation anatomical structure area when the instrument operates in the variation anatomical structure area, and operating according to the prompt. According to the method, by establishing the corresponding relation between the imaging examination and the endoscopic surgery visual field, the vein pipeline structure of the key operation in the surgery is accurately and effectively positioned, and important conditions are provided for more accurate operation of the surgical operation.