Objective To analyze the characteristics of intestinal flora of personnel stationed on an island, so as to lay the foundation for maintaining the intestinal microecological balance of personnel stationed on island and provide accurate medical security. Methods Several subjects stationed on an island and several subjects from coastal areas were enrolled by random and sampling method, and their fecal samples were sequenced by 16S rRNA high-throughput sequencing. Diversity and composition of gut microbiota in 2 cohorts of personnel were compared. Results Alpha diversity analysis of intestinal flora showed that the abundance of intestinal flora in subjects stationed on the island was significantly higher than that of subjects from coastal areas. Beta diversity analysis indicated significant differences in the composition of intestinal microbial communities between the subjects stationed on the island and those from coastal areas (P＝0.001). The abundance of the Bacteroidota in the intestinal tract of subjects stationed on the island was significantly lower than that of subjects from coastal areas (30.8% vs 48.3%, P＜0.001), while the abundance of the Proteobacteria was significantly higher than that of subjects from coastal areas (28.3% vs 10.2%, P＜0.001). After multiple hypothesis testing correction, it was found that the abundance of the Bacteroides, Roseburia, Alistipes, and Parabacteroides in the intestines of subjects stationed on the island decreased significantly, while the abundance of the Prevotella, Escherichia-Shigella, Citrobacter, and Eubacterium_coprostanoligenes increased significantly. Conclusion The special environment of islands affects the characteristics of intestinal flora of personnel, and the intestinal microecological health needs precise maintenance.