In order to analyze the effect of Rhodobacter capsulatus and Bacillus cereusr on the intestinal microorganism of Litopenaeus vannamei, the experiment was carried out for 30 days in order to study the effect of two probiotics on the culture and feeding of L. vannamei. The 16s rDNA V4 region of intestinal microorganism of L. vannamei was sequenced with high throughput in the later stage of feeding to analyze the structural characteristics of intestinal microflora of L. vannamei fed with different probiotics, and combined with the macroscopical indexes of the growth rate of body mass and the cumulative mortality of the prawn after poisoning. The results:①the range of OTU was 374~506, in which the number of OTU in intestinal tract of the prawn was the lowest in blank group, and the number of OTU in intestinal tract of shrimp was relatively high in two groups after feeding probiotics; ②at the level of phylum classification, the number of Proteobacteria was the highest in three groups, the CK group was mainly Proteobacteria and a small amount of Bacteroidetes, the Bc group was mainly Proteobacteria, Bacteroidetes, Tenericutes, Firmicutes and Gemmatimonadetes, the Rc group was mainly Proteobacteria, Bacteroidetes, Firmicutes, Acidobacteria, Actinobacteria, Fusobacteria and Cyanobacteria; ③the results of rarefaction curve and Shannon index showed that the species abundance and complexity of blank samples were the lowest, and the sample abundance and complexity of B.cereus group were relatively high; ④PCA analysis showed that the microbial composition of the samples of R. capsulatus group and blank group was close. Combined with the results of macroscopical growth rate of shrimp body mass and cumulative mortality after poisoning, it can be seen that the effect of B. cereus on intestinal microflora of L. vannamei is more significant than that of R. capsulatus, and the probiotic effect is better. The results showed that feeding probiotics could augment the abundance of intestinal microflora of L. vannamei, inhibit the growth of harmful bacteria such as Vibrio, increase the growth rate of body mass and reduce the mortality of prawn, so as to achieve the probiotic effect. The effect of feeding B. cereus was better than that of R. capsulatus.