Metro systems are vulnerable to flooding during rainstorms and this situation worsens when a subsiding environment prevails. This study adopts the interval fuzzy analytic hierarchy process (FAHP) incorporated with fuzzy clustering analysis (FCA) to assess the flood risk of metro systems in subsiding environments, considering both the regional subsidence of the ground and the longitudinal settlement along metro lines as assessment factors. Shanghai metro system is analysed as an example by using the proposed method (the FAHP–FCA approach) together with the geographical information system (GIS). The assessment results show that more than 30% of metro lines in Shanghai are at a high risk of flooding, and the high-risk regions of metro lines are located in urban centres. The ratio of high-risk regions identified by the FAHP–FCA approach exceeds that obtained using the existing FAHP approach, which indicates that the FCA-FAHP approach can capture high-risk metro systems in Shanghai. Moreover, the comparison also shows that subsiding environments exacerbate the flood risk of metro systems. It is proposed that, to mitigate the risk of flooding, subsidence environments should be considered in more detail.