Hypertriglyceridemia (HTG) is a common and significant contributor to acute pancreatitis (AP). Caffeine has been reported to have a protective effect against pancreatic disorders. However, the role of caffeine in hypertriglyceridemia acute pancreatitis (HAP) is still unknown. To investigate a new understanding of the relationship between caffeine and gut microbiota in HAP development. Using multi-omics analysis of 71 HAP and HTG patients, their characteristics of intestinal microecology were detected. HTG mice models were established through either pharmacological induction (P-407 intraperitoneal injection) or genetic ablation of GPIHBP1 (GPIHBP1−/−). Genes deferentially expressed in the gut were identified by RNA sequencing and the role of caffeine in reshaping gut microbial networks was investigated. Caffeine levels decreased significantly in HAP patients and were inversely correlated with the severity of HAP. Caffeine maintained the intestinal homeostasis and attenuated HAP through a gut microbiota-dependent manner in the mouse model. Specially, the commensal Faecalibacterium prausnitzii, which contributed most in distinguishing the differences between HTG and HAP patients, has been found to be related to the effect of caffeine on alleviating HAP. RNA sequencing combined with TLR4−/− mice revealed that TLR4/NLRP3 may be the key signaling pathway for caffeine to maintain intestinal homeostasis and alleviating HAP. This study reveals the gut metabolites and microbiota characteristics of HAP and HTG patients, and explores the therapeutic potential of caffeine against HAP from the perspective of gut microbiota.