In order to solve the problem that the video depth and stereoscopic sense of the video obtained by the short baseline binocular endoscopic imaging system are weak in the naked eye 3D display device, by analyzing the parameters of the binocular endoscope and the parallax of the image pair in the stereoscopic video, a stereo video correction and parallax adjustment method based on the short baseline binocular endoscopic imaging system is proposed. Firstly, the camera of the binocular endoscope system is calibrated to obtain the camera parameters and the position parameters between cameras; Secondly, the camera video is corrected by using the obtained parameters, and then the image parallax is adjusted according to the parameter requirements of the naked eye 3D display device for the video source, so as to finally obtain the real-time display stereoscopic video of the binocular endoscope system which meets the requirements of the naked eye 3D stereoscopic display device and is suitable for human eyes. The feasibility of the method is verified by experiments. A short baseline binocular endoscope imaging system with a baseline distance of 8mm is actually built. The original parallax range is (0,64) pixels, which can reach (-30,30) after parallax adjustment. The two-way parallel video processing is 25 frames/s for real-time display. Matching with the naked eye 3D stereoscopic display system designed in the laboratory, real-time naked eye 3D imaging of medical endoscope with obvious stereoscopic feeling can be realized.