The invention provides a stereoscopic endoscope system which comprises a stereoscopic endoscope, a light source, an image collecting processor and a 3D displayer. The stereoscopic endoscope is connected with the light source and the image collecting processor, the image collecting processor is connected with the 3D displayer, the stereoscopic endoscope comprises two light paths, an object lens, a rotating mirror, an ocular lens, an adapter and a CCD are fixed to each light path in sequence, cables stretching out of the rear ends of the two CCDs are combined to be one cable and are connected with the image collecting processor, and a cable connected with the light source can be connected fast with a stereoscopic camera shooting part and is guided out of a rear end. The stereoscopic endoscope system has the advantages that the two light paths are adopted in the stereoscopic endoscope system, two sets of images are formed and output, signals are collected and processed, standard 3D digital signals are directly output, and the check and treatment effect of diseases is improved. Light sources and image collecting processors are integrated and optimized in one light source and one image collecting processor from original two sets of light paths respectively, the structure is reduced, and cost is lowered.