Due to the climate change induced extreme rainfall, urban flooding risk is one of the major concerning risk in the near future with accelerating occurrence frequency and intensity. To enhance the city resilience against flooding risk, this paper proposed a GIS-based spatial Fuzzy Comprehensive Evaluation (FCE) framework to quantify multiple impact factors in an integrated ArcGIS platform. This assessment method incorporates the hydrodynamic drainage simulation results for further calculation of 6 methodically picked evaluation indices such as the transportation attenuation and residential security index, which helps to reduce the subjective effect for the integrated comprehensive risk assessment. The detailed application in SA city validates the effectiveness of the adopted GIS-based FCE method, and the results illustrate the areas with higher risk levels reasonably coincide with severe inundation situations and dense hazard-bearing bodies. This systematic evaluation framework can support applicable references for further extension to other cities to efficiently allocate limited resources especially under flooding rescue conditions.