Farmed P. vannamei of the same age displayed significantly different body sizes in a high nitrite pool. To examine the intestinal microbiota structure and function of shrimps and whether the growth differences between them were related to intestinal microbiota in high nitrite environment, intestinal and seawater samples were collected from rapid growth (RG), normal growth (NG), and slow growth (SG) shrimps in the high nitrite pool. The 16s sequencing analysis found that the bacterial community diversity of SG was different from that of RG and NG. PCoA analysis showed that the community composition of NG was more similar to RG than SG. The LEFse difference analysis revealed that Flammeovirgaceae, Flavobacteriaceae, and Planctomycetaceae had a high abundance in the RG, while Desulfovibrionaceae, Shewanellaceae and Vibrionaceae were significantly enriched in SG. This study found that the difference in nitrogen metabolism capacity of intestinal colonies in the high nitrite environment leads to the consequence of different growth rates. And the study will provide instruction in the industrial farming of shrimp.