The main reason for serious consequences caused by disasters is “insufficient emergency preparedness and obvious system vulnerability”. To ensure the safe operation and maintenance of the high-speed railway in goaf sites and achieve effective hierarchical management, the vulnerability theory was introduced, based on the system approach, to explore the characteristics of hierarchical evolution. Firstly, based on the analysis of the internal and external disturbances of the high-speed railway construction system with underlying goaf areas, the vulnerability characteristic elements were defined, and a conceptual vulnerability model was proposed. Secondly, based on the literature research, accident cases, and standards and specifications, 25 factors affecting vulnerability were identified and a two-dimensional cross matrix was used to establish a vulnerability evaluation index system. Then, ISM was used to build hierarchical relationships among indicators, analyze the vulnerability characteristics of direct factors, indirect factors and essential factors, and a vulnerability evolution analysis framework was proposed. Finally, the Taiyuan–Jiaozuo high-speed railway project was selected for hierarchical and progressive vulnerability management. The study analyzed the coupling effect and evolution mechanism of various elements of the safety management system under external disturbances, identified the weak links of the high-speed railway system in the goaf site, and provided a decision-making basis for continuous dynamic optimization and emergency response technology, which complied with the strategic policy of sustainable development.