A sediment-water-Vallisneria natans system was built within a simulating lake system, where phospholipid fatty acids (PLFAs) method was used to determine the changes in sediment microbial community structures in the submerged plant V.natans at different growth stages.The results showed that during the growth of V.natans, the organic matter content decreased first and then increased.The concentrations of total phosphorus, organic phosphorus and inorganic phosphorus decreased by 8.97%, 7.81% and 10.28%, respectively, during the growth period.The microbial activity and total phosphorus in sediments showed extremely significantly negative correlation.In the early exuberant period, microbial activity in the experimental group was greater than the control group, while the decline in the microbial activity of the control group was slightly higher than the experimental group.Microbial community structure in the sediments of different periods showed significant differences.Bacteria were the main part of the total sediment microbes, accounting for 76% to 84% of the total microbial.As to bacterial distribution, gram-positive bacilli were predominant.The percentage of gram-positive bacteria and fungi increased with the growth of the V.natans.