The three-dimensional medical electronic endoscope system is widely used for medical diagnosis, minimally invasive surgery and medical training. The geometric distortions during the visualization of the three-dimensional endoscope will affect the relative size and distance estimation accuracy of the nidus for the medical staff, and also may be one of the important factors inducing the visual discomfort. Existing researches only focused on the distortions of the two-dimensional image and its correction. The three-dimensional space geometric distortions during the visualization due to the mismatching of the three-dimensional display system and the characteristics of human eye three-dimensional perception are usually ignored. Based on the analysis of three-dimensional medical electronic endoscope image acquisition, display and perception process, the model of three-dimensional medical electronic endoscope system is established. The ideal three-dimensional endoscope image visualization is the equally magnified virtual space based on the real-world space in all dimensions, and the matching of parameters between three-dimensional endoscope image capture and visualization can achieve this goal, and finally realize the precise visual perception and well visual comfort. The results may provide some theoretical guidance for more precise and comfortable utilization of the three-dimensional image capture and visualization in medical domain.