The invention discloses a three-dimensional endoscope system compatible with two-dimensional endoscopes. The three-dimensional endoscope system comprises a first object lens, a second object lens, a first image transmission column, a second image transmission column, a first image diaphragm, a second image diaphragm, a first focusing lens group, a second focusing lens group, a first deflection prism, a second deflection prism, a first cylindrical lens and a second cylindrical lens. The three-dimensional endoscope system has the advantages that the first deflection prism is used for reflectingfirst light beams which are received by the first focusing lens group and are projected from the first focusing lens group, the second deflection prism is used for reflecting second light beams whichare received by the first focusing lens group and are projected from the second focusing lens group, accordingly, the distances between the optical axes of the first light beams and the second light beams can be changed, and the three-dimensional endoscope system can be matched with image sensors of two-dimensional endoscope systems; the first cylindrical lens is used for compressing the first light beams reflected from the first deflection prism, the second cylindrical lens is used for compressing the second light beams reflected from the second deflection prism, and accordingly flattened first images and flattened second images can be acquired by first light sensing regions and second light sensing regions of the image sensors.