Nitrite is the main environmental pollutant that endangers shrimp culture. Intestinal health is essential for the disease resistance of shrimp. In this study, Litopenaeus vannamei shrimps were separately exposed to 1 and 5 mg/L of nitrite stress for 48 h, and then the variations in intestinal health were investigated from the aspects of histology, antioxidant, immunity, energy metabolism, and microbial community status. The results showed that nitrite stress damaged intestinal mucosa, and 5 mg/L of nitrite induced more obvious physiological changes than 1 mg/L. Specifically, the relative expression levels of antioxidant (ROMO1, Nrf2, SOD, GPx, and HSP70), ER stress (Bip and XBP1), immunity (proPO, Crus, ALF, and Lys), inflammation (JNK and TNF-α), and apoptosis (Casp-3 and Casp-9) genes were increased. Additionally, intestinal energy metabolism was activated by inducing glucose metabolism (HK, PK, PDH, and LDH), lipid metabolism (AMPK and FAS), tricarboxylic acid cycle (MDH, CS, IDH, SDH, and FH), and electron transfer chain (NDH, CytC, COI, CCO, and AtpH) gene transcription. Further, the homeostasis of intestinal microbiota composition was also disturbed, especially the abundance of some beneficial genera (Clostridium sensu stricto 1, Faecalibacterium, Romboutsia, and Ruminococcaceae UCG-010). These results reveal that nitrite stress could damage the intestinal health of L. vannamei by destroying mucosal integrity, inducing oxidation and ER stress, interfering with physiological homeostasis and energy metabolism, and disrupting the microbial community.