As a typical complex network system, the operating environment of rail transit network (RTN) is complex and demanding. This study aims to accurate assess the weaknesses and vulnerability of RTN, which is crucial for ensuring its smooth operation. Taking Chongqing Rail Transit (CRT) as an example, this study developed a network topology model using the spatial L method and analyzed the network structure characteristics, along with the importance of key nodes under different indicators, based on complex network theory. Additionally, this study analyzed the geographical spatial distribution characteristics of nodes based on the topography and urban spatial structure of Chongqing. Then, this study classified the nodes in the RTN according to basic topological indicators, namely degree, betweenness centrality, network efficiency, and passenger flow volume (PFV). The results indicated six cluster of nodes, reflecting the variability in node vulnerability concerning overall influence (providing alternative paths, reducing path length), regional aggregation capacity, and transportation capacity. Finally, this study proposed targeted management strategies for different clusters of nodes and their respective geographical locations, providing necessary references for rational planning, safety protection, and sustainable construction of RTN.