Abstract: In recent years, small greenhouse has been a hot model of Litopenaeus vannamei culture. In order to elucidate the structure and changes of the microbial community in the rearing water of L. vannamei culture in small greenhouse and explore the reasons for high yield and high efficiency of this model, we analyzed the composition and function of the microbial community on 2^nd, 44^th, 69^th and 96^th day of water in the small greenhouse based on 16S rRNA sequencing results. The results show that the richness and diversity of water microbial community at late stage of small greenhouse were significantly higher than those at early stage. During the whole culture process, the dominant bacteria at the phylum level were Proteobacteria, Bacteroidetes and Actinobacteria, among which the abundance of Proteobacteria increased significantly on 69^th day, and the abundance of Actinobacteria increased at early stage but decreased at later stage. At genus level, the abundance of Candidatus_Aquiluna was the highest on 2^nd day (28.7%). Marivita was enriched at middle stage, with the highest abundance on 69^th day (9.94%). The abundance of Flavobacterium gradually increased with the culture time, reaching the highest on 96^th day (11.63%). PICRUSt2 predicts the function of the microbial communities, and the abundances of metabolic function in the top 20 were significantly higher on 69^th and 96^th day than on 2^nd day. In particular, the functions of terpenoids and polyketides metabolism, lipid metabolism, xenobiotics biodegradation and metabolism were highly enriched. Through FAPROTAX identifying, the abundance of chemoheterotrophy increased significantly at the late stage. The correlation analysis of environmental factors shows that total nitrogen (TN) and chemical oxygen demand (COD) had the greatest impacts on the microbial community structure in greenhouse model. Microorganisms such as Marivita, Candidatus_Aquiluna and Rhodopirellula played the roles in sequestration of carbon and reduction of nitrogen and phosphorus. In conclusion, under the high density and high nitrogen and phosphorus culture conditions, the water microbial community in the small greenhouse played an important role in maintaining the stability of water environment and enhancing the immunity and disease resistance of prawns.