Floods in the metro system have caused catastrophic damages in mega-cities, especially in subsiding environment. This data in brief gives a detailed description for the calculation of judgment matrixes during decision making process for the flood risk assessment of the metro system. The data source of the assessment factors is provided. The analytical hierarchy process (AHP) and interval fuzzy AHP (FAHP) are used to calibrate the weights of assessment factors. The fuzzy clustering analysis (FCA) method is used to modify the weights obtained from AHP and interval FAHP. The data presented herein was used for the article, titled “Flood risk assessment of metro systems in a subsiding environment using the interval FAHP–FCA approach” Lyu et al. (2019) [1].