To study the relationships between water depth, inundation duration, and the growth process of Phragmites australis in Hankou floodplain, the existing growth dynamic phenological model was improved, in which flooding stress effects of water depth and inundation duration on Phragmites australis growth were considered. The improved model was applied to simulate the growth process of Phragmites australis in the Hankou floodplain under different flooding stress conditions. The results showed that the above-ground biomass of Phragmites australis decreased sharply due to flooding stress during the flood season, indicating that the effect of flooding stress should not be ignored; with the increases of the water volume and inundation duration, the above-ground biomass reduction rate of Phragmites australis caused by flooding stress increased; there were power function relationships between the above-ground biomass reduction of Phragmites australis, the inundation duration, and the duration with water depth greater than 2 m, and the flooding stress caused by water depth exceeding the inundation threshold was dominant.