Taking the typical beach equatic plant, phragmites australis, as the study object, a growth dynamic model of Phragmites australis considering flooding stress and a hierarchical model of biomass were established in this study. A calculation method was then proposed of equivalent Manning roughness which considered the growth dynamic of Phragmites australis. Based on this method, the differences in equivalent Manning roughness under different Phragmites australis growth processes and flooding conditions were analyzed. An empirical formula was established between the equivalent Manning roughness, aboveground biomass of Phragmites australis, relative submergence degree under the non-submerged condition. The results show that the growth dynamic model could effectively simulate the change processes of aboveground biomass and morphology parameters of Phragmites australis, with the Nash efficiency coefficient ranging between 0.85 and 0.94.Similar vertical distribution patterns existed in biomass and flow blocking area of Phragmites australis. With a critical relative height of 0.3, the flow blocking area of stems was characterized by more below and less above, and the flow blocking area of leaves was characterized by less below and more above. The total flow blocking area and aboveground biomass of Phragmites australis were approximately uniformly distributed below a relative height of 0.7.The calculated maximum equivalent Manning roughness was approximately 0.300. Under the effect of flooding stress, the aboveground biomass of Phragmites australis decreased, resulting in a 10.0%~29.1% reduction in equivalent Manning roughness under the same water depth.