How to qualitatively and quantitatively evaluate the ability of the whole subway system to maintain the maximum normal operation has become a noteworthy topic. In this study, the hypergraph space structure of Nanjing subway network is used for research. This study uses the method of time-space evolution mechanism to dynamically and quantitatively analyze the gradual change characteristics of Nanjing subway system vulnerability under the influence of time and space. In addition, this study also makes static and dynamic comparative analysis on the vulnerability of a subway system by using connectivity rate and trip efficiency index, which provides new analysis methods and ideas for the study of a subway system network. The results show that although the overall structure of Nanjing’s subway network shows a loose trend, as Nanjing’s subway is still in a rapid development stage, it can be seen from the long-term planning of Nanjing’s subway that the construction of Nanjing’s subway ring line will be strengthened after the completion of the connection between the main city and the suburbs. Therefore, the vulnerability of the subway system should be reduced and the reliability will be improved.