The invention discloses a shunt automatic detection and dustproof end cover automatic assembling system. The system comprises a rack, wherein a detection table and a cover-installing table are arranged on the rack, a detection fixing device and a cover-installing fixing device are arranged on the rack, and a piece rotating device is arranged between the detection table and the cover-installing table; a common end connector and a branching end connector are arranged on the rack and are jointly in signal connection with an optical path detector, and a common end insertion controller and a branching end insertion controller are arranged on the rack; and a cover-installing device is arranged on the rack, and the optical path detector is in signal connection with the cover-installing device. According to the system, optical path connection between each branching end and a common end can be detected sequentially on the detection table, the cover-installing device performs dustproof end coverinstallation on the common end and qualified branching ends according to the optical path connection, shunt detection work and dustproof end cover installation work are automatic, the efficiency of detection and dustproof end cover installation is improved, and the error rate is reduced.