During the rainy season, heavy rainfall will lead to urban waterlogging disasters, which have a great impact on the environment. In addition, the continuous flood disaster has seriously affected the operation and safety of urban subways and the living environment of human beings. After the flood disaster, the underground railway and its surrounding environment are highly vulnerable systems with strong uncertainty, ambiguity, and complexity. Therefore, it is the key issue to perform an environmental vulnerability assessment of the rainstorm waterlogging disaster in urban rail transit for environmental estimation and emergency decision-making. Based on a large amount of literature research and environmental assessment experience, the index system for rainstorm waterlogging environmental vulnerability assessment has been constructed, which includes 5 secondary indexes and 25 tertiary indexes. Moreover, the entropy weight theory is improved, and the matter-element theory is optimized to construct the environmental vulnerability assessment model of the rainstorm waterlogging disaster. The Nanning Metro Line 1 is analyzed as a typical case study. The results show that the new environmental vulnerability assessment model is perfect for case studies, and the evaluation result is level Ⅲ. Furthermore, the application results of the environmental vulnerability assessment show that the main influencing factors are emergency training drills and crisis response learning. Overall, this assessment method can be extended to similar applications of environmental vulnerability assessment in flood disasters.