An input device detection system includes a foundation, a cover plate and a trajectory detection plate. The foundation includes a base plate and plural first retractable rods. The base plate has a top surface, a bottom surface and a detection hole. The input device is pushed by the plural first retractable rods along a horizontal direction. The input device is pushed by plural second retractable rods of the cover plate along a vertical direction. The trajectory detection plate is located under the base plate. An optical sensing module of the input device emits a light beam. The light beam is transmitted through the detection hole and projected to the trajectory detection plate. When the trajectory detection plate is moved relative to the foundation and the light beam is reflected to the optical sensing module by the trajectory detection plate, a trajectory signal is generated.