The invention provides a control method and system of a route trigger order. The method comprises the steps that S1, a unique operating path of a train is determined; S2, whether the train has a combination scene of multiple routes is judged, wherein when the train does not have the combination scene of the multiple routes, the step S3 is executed, and when the train has the combination scene of the multiple routes, the step S4 is executed; S3, route data are stored, the route trigger order is controlled according to the stored data, and the steps in the method are completed; S4, the route combination of the unique path is extracted; S5, the route combination is divided into a near-end route and a far-end route, the far-end route is defined as a dependency route of the near-end route, and a dependency route relation is stored; S6, the route trigger order is controlled according to the stored dependency route relation. According to the control method and system, a conventional control method of the route trigger order is improved, manual intervention is reduced, and the automation degree and operation efficiency are improved.