Emergent plants can not only absorb nutrients from water and sediment as a "sink" during the growth period, but also release nutrients such as nitrogen and phosphorus into the water environment as a "source" during the decline period. If the biomass is large, it may cause "secondary pollution" of water. In order to explore the nutrient release rule of typical emergent plants in Hengshui Lake and the microbial mechanism affecting plant decomposition, the dominant species Phragmites australis and Typha angustifolia were selected as the research objects, and the decomposition bag method was used to carry out in-situ decomposition tests in Hengshui Lake at the end of February 2023. The "vertical decomposition" of plants was simulated in the experimental group which was not in contact with water surface, and the decomposition of emergent plants was simulated in the experimental group which was flooded under water surface. The results showed that: (1) The decomposition rates of P. australis and T. angustifolia were significantly different under flooded and non-flooded conditions (p< 0.01). The decomposition of P. australis and T. angustifolia was more conducive to the decomposition of P. australis and T. angustifolia, but the long-term flooding might lead to the accumulation of elements. (2) The decomposition rate of T. angustifolia was faster than that of P. australis, because the decomposition rate was positively correlated with the initial N and P contents and the relative abundance of nitrogen and phosphorus cycling genes., and negatively correlated with the initial cellulose, lignin and soluble sugar contents. (3) The abundance of nitrogen fixing genes increased gradually with the increase of decomposition degree, and the increase of N content in P. australis and T. angustifolia litter was positively correlated with the nitrogen fixing genes of nitrogen fixing microorganisms.