Aimed at insuring the ecological base flow of Jinling river and enhancing the groundwater circulation rate and intensity,the paper took flood infiltration experiment for example and applied the mean of numerical simulation to study the storage capacity of flood infiltration. The results indicate that about 24.9% of the infiltrated flood is used to increase the aquifer storage, 36.3% of the infiltrated flood finally flows into Jinling river and increases its ecological base flow; the infiltrated flood is stored in aquifer and retards for 200 days. Flood infiltration is beneficial to making full use of flood resources, the method redistributes water resources spatially and temporally in the study area and shows remarkable storage effect.