Abstract:[Background] Gut microbiota and exercise both are closely related to human health, but the effect of high-intensity interval training on gut microbiota is still limited. [Objective] To explore the effect of high-intensity interval training on gut microbiota, moreover provide reference for the prevention and treatment of the whole people’s physical health and gut microbiota related diseases. [Methods] 68 volunteers were recruited for high-intensity interval training 3 times a week for 12 weeks, fresh feces were collected before and after exercise, and 16S rRNA gene high-throughput sequencing techniques were used to analyze the gut microbiota. [Results] After 12 weeks of high-intensity interval training the Shannon index of gut microbiota increased significantly (P≤0.001); PCoA analysis showed that there were significant differences; the level of pre-exercise genus Faecalibacterium, Unclassified-f-Enterobacteriaceae, Lactobacillus, Unclassified-f-Pasteurellaceae, Acinetobacter; the level of order Enterobacteriales, Pseudomonadales; the level of family Enterobacteriaceae, Lactobacillaceae, Moraxellaceae abundance was significantly higher than that after exercise; but after exercise, the level of genus Ruminococcaceae-UCG-014, Eubacterium-ruminantium-group, Lachnospiraceae-UCG-010, Tyzzerella-3, Unclassified-o-Bacteroidales; the level of family Unclassified-o-Bacteroidales abundance was significantly increased. [Conclusion] 12 weeks high-intensity interval training can effectively alter the gut microbiota, but the effect of regulation on male and female students is different. The abundance of gut microbiota and beneficial microbiota increased significantly.