The invention is applicable to the technical field of transmission networks, and provides a transmission network physical same-route hidden danger checking and avoiding system and method, the system comprises three subsystems, namely a pipeline system, a manufacturer network management system and an integrated resource system, and the pipeline system is used for risk checking of cross-network-management same-route; the transmission optical cable link information is called through a pipeline system, and the data is integrated into a transmission optical cable segment table; meanwhile, risk traversal of the same route is carried out on the optical cables in the transmission optical cable segment table, and the risk ratio of the same route is calculated to form a same-route optical cable pair, a transmission optical cable segment table is formed, physical same-routing hidden trouble checking of the transmission network is realized; and then the manufacturer network management system modifies the port data of the optical cable according to the new transmission optical cable segment table, increases the management of the risk link group, checks and reminds the risk link group when the service configuration is passed, and issues the configuration after confirmation, thereby realizing the avoidance of the hidden trouble checking of the physical same route of the transmission network.