The frequent occurrence of urban flooding in recent years has resulted in significant damage to ground-level infrastructure and poses a substantial threat to the metro system. As the central city’s core transportation network for public transit, this threat can have unpredictable consequences on travel convenience and public safety. Therefore, assessing the risk of urban flooding in the metro system is of utmost importance. This study is the first of its kind to employ comprehensive natural disaster risk assessment theory, establishing an assessment database with 22 indicators. We propose a GIS-based method combined with the analytical hierarchy process (AHP) and an improved entropy weight method to comprehensively evaluate the urban flood risk in Changchun City’s metro systems in China. This study includes a total of nine metro lines, including those that are currently operational as well as those that are in the planning and construction phases, situated in six urban areas of Changchun City. In this study, we utilize the regional risk level within the 500 m buffer zone of the metro lines to represent the flood risk of the metro system. The proposed method assesses the flood risk of Changchun’s rail transit system. The results reveal that over 30% of Changchun’s metro lines are located in high-risk flood areas, mainly concentrated in the densely populated and economically prosperous western part of the central city. To validate the risk assessment, we vectorized the inundation points and overlaid them with the regional flood risk assessment results, achieving a model accuracy of over 90%. As no large-scale flood events have occurred in the Changchun rail transit system, we employed receiver operating characteristic (ROC) curves to verify the accuracy of the flood risk assessment model, resulting in an accuracy rate of 91%. These findings indicate that the present study is highly reliable and can provide decision makers with a scientific basis for mitigating future flood disasters.