The invention belongs to the technical field of rail transportation, and particularly relates to a system linkage method after train jam in rail transportation. The method comprises the steps of: intercoupling special systems arranged in railway stations, intervals and a control center; monitoring the train running state by a train automatic monitoring system, transmitting collected train jam position information to a comprehensive monitoring system of the control center; and selecting starting a railway station interval jam model or a railway station track running region jam model by the comprehensive monitoring system of the control center according to the collected jam position information. The system linkage method has the advantages that a set of rapid response plans after trains are jammed at the railway stations or the intervals is established, so as to improve the automation degree of rail transportation operation, realize the functions of optimizing the management, saving labors and increasing efficiency as well as lowering the function of manual false operation, improve the comprehensive response speed of systems of the rail transportation, and guarantee safety of persons and equipment.