[Objective] This research aims to investigate the diversity of microbial community structure in different seagrass growth periods, and to analyze the internal factors that lead to the differences in microbial community structure.[Methods] The rhizosphere sediments of seagrass and unvegetated areas surface sediments were collected. High throughput sequencing (Illumina MiSeq Platform) was used to analyze the microbial community characteristics of rhizosphere and unvegetated areas at different seagrass growth stages.[Results] The difference in microbial community structure was driven by the growth period of seagrass and whether seagrass was colonized. At the maturation stage of seagrass, Propionium was significantly enriched in the roots of Z. marina and Z. japonica, with a relative abundance of 11.58% and 14.26%, respectively. In the seedling stage of seagrass, Desulfobulbaceae was enriched at the seagrass roots (Z. marina:2.299%, Z. japonica:4.092%). The relative abundance of Sulfurovum was higher in the rhizosphere during the decline stage of seagrass (Z. marina:5.624%, Z. japonica:3.749%). In addition, the growth period of seagrass had the greatest explanatory power for the differences in microbial community structure (R²=0.20335, P=0.002). The results of PICRUSt2 function prediction showed that all functional genes showed the same trend in different growth stages of seagrass, but the abundance showed the result of seedling stage > mature stage > decline stage.[Conclusion] The microbial community structure of seagrass bed sediments in Swan Lake presented different diversity characteristics at different growth stages of seagrass, with obvious rhizosphere effect and no significant difference in the rhizosphere microbial community of different species of seagrass, which was not species-specific.