Abstract: Provided by the present invention are a method and system for automatically optimizing 3D stereoscopic perception, and a medium. The method comprises the following steps that are executed successively: step 1: given current left and right images, calculating a stereo disparity to generate a disparity map; step 2: calculating a depth value corresponding to each individual pixel by using the calculated disparity; step 3: calculating a depth distance of a target to be observed; step 4: acquiring corresponding left and right image displacement values by using the depth distance calculated in step 3; and step 5: applying the acquired image displacement values into a 3D display. The beneficial effect of the present invention is that: the method for automatically optimizing 3D stereoscopic perception according to the present invention solves fatigue and dizziness that are easily generated during the use of a 3D endoscope.