PURPOSE: This study aimed to explore the characteristics of intestinal microflora polymorphism in postmenopausal women, and to determine the pathophysiological changes of gene polymorphism of intestinal flora and bone metabolism in postmenopausal osteoporosis (PMOP) patients. METHODS: A total of 104 postmenopausal women with PMOP or normal bone density were included. Lifestyle, hip T-score, bone metabolism indexes (25(OH)D, PTH, β-CTX, PINP), intestinal mucous membrane barrier function (diamine oxidase, D-lactic acid, LPS), gene polymorphisms, and characteristics of gut microbiota were examined. RESULTS: Women with PMOP had reduced physical activity, less dietary protein and calcium intake, lower levels of 25(OH)D, hip T-score, and BMD, but PMOP group had increased total energy and fat intake, and higher levels of PTH, β-CTX, diamine oxidase, D-lactic acid, and LPS ( CONCLUSION: The incidence of PMOP was closely associated with fecal microbial compositions and intestinal functional changes. The present findings supported potential applications of gut microbiome analysis for early diagnosis of PMOP, and provided potential therapeutic targets.