High-temperature (HT) is a critical influencing factor in shrimp aquaculture and serves as a key trigger for frequent disease outbreaks in shrimp. As a core organ for digestion, absorption and immune defense, the intestine's functional homeostasis is the key foundation for shrimp health. Therefore, in this study, the shrimp Litopenaeus vannamei were continuously exposed to HT stress at 33 °C for 7 days, after which the changes in intestinal functional homeostasis were investigated based on the mucosal integrity, immune signaling, and microbial community. The results showed that HT stress caused intestinal epithelial detachment and mucosal damage, as well as the disruption of the mucus barrier, including the upregulation of MUC2, MUC3A and MUC3B genes and the downregulation of MUC1 and MUC4 genes. Additionally, oxidative stress-related genes, such as the expressions of ROMO1, Nrf2, GPx and HO1 were upregulated, while the expression of SOD was downregulated; antimicrobial genes, such as the expressions of Crus and proPO were upregulated, whereas the expressions of ALF, Pen3 and Lys were downregulated; inflammatory genes (JNK and NF-κB) and autophagy genes (Atg3, Atg12, Beclin1 and Hsc70) expression were all upregulated. In terms of intestinal microbiota, microbial diversity showed no significant changes, but the abundance of community composition was perturbed, particularly the homeostasis of putative harmful bacteria (Vibrio and Photobacterium) and beneficial bacteria (Bacteroides, Bacillus, Lactobacillus, and Lactococcus). Additionally, the phosphotransferase system (PTS) function of the intestinal microbiota was enhanced, while the functions such as N-glycan biosynthesis and glycosaminoglycan degradation were weakened. These results demonstrated that HT stress disrupted intestinal functional homeostasis by inducing mucosal damage, disrupting the mucus barrier and immune responses, activating oxidative stress, inflammation, and autophagy signaling, and reshaping the microbial community.