To explore the microbial community structure and changes in the intestine of Litopenaeus vannamei and its aquaculture environment during the cultivation process, Illumina MiSeq high-throughput sequencing platform was used to analyze the microbial community in the gut of L. vannamei at age of 46 and 86 days, and its aquaculture water and sediments correspondingly, based on the 16S rRNA sequence. The results showed that the Shannon-Wiener diversity indexes in water samples were significantly lower than those in sediments and shrimp intestines. We detected 35 phyla, 70 classes, 152 orders, 274 families and 420 genera that existed in water, sediments and L. vannamei intestines. There were more common microbes in the intestines of L. vannamei and the sediments than those in the water. The microbial community structure of water, sediments and L. vannamei intestines changed when culturing time prolonged, the different phyla of 46 and 86 d were Actinobacteria, Chlorobi, Fibrobacteres, Planctomycates and TM6. Relative abundance increased with time. However, the dominant flora was relatively fixed. At the phylum level, Proteobacteria, Bacteroidetes, Actinobacteria were the three dominant categories in all three kinds of samples. At the class level, Alphaproteobacteria, Betaproteobacteria and Actinobacteria were the dominant categories. In addition, L. vannamei intestines and sediment had the common dominant classes of Deltaproteobacteria, Gammaproteobacteria and Gemmatimonadetes. From the classification levels of order, family and genus, the microbial community relative abundance in various samples presented differences, so that few common categories showed overlapping dominance in samples except unclassified genera, which was the most abundant in all the samples. Besides, hgcI_clade was the dominant genus in the water, Ambiguous_taxa was the predominant genus in the L. vannamei intestines and sediments. These results further explained the correlation of the microbial community structure in intestine of L. vannamei and its aquaculture environment, and also showed the differences that emerged during the culture process.