Reduced bone mineral density (BMD) is associated with an altered microbiota in senile osteoporosis. However, the relationship among gut microbiota, BMD and bone metabolic indexes remains unknown in postmenopausal osteoporosis. In this study, fecal microbiota profiles for 106 postmenopausal individuals with osteopenia (n=33) or osteoporosis (n=42) or with normal BMD (n=31) were determined. An integrated 16S rRNA gene sequencing and LC-MS-based metabolomics approach was applied to explore the association of estrogen-reduced osteoporosis with the gut microbiota and fecal metabolic phenotype. Adjustments were made using several statistical models for potential confounding variables identified from the literature. The results demonstrated decreased bacterial richness and diversity in postmenopausal osteoporosis. Additionally, showed significant differences in abundance levels among phyla and genera in the gut microbial community were found. Moreover, postmenopausal osteopenia-enriched N-acetylmannosamine correlated negatively with BMD, and distinguishing metabolites were closely associated with gut bacterial variation. Both serum procollagen type I N propeptide (P1NP) and C-terminal telopeptide of type I collagen (CTX-1) correlated positively with osteopenia-enriched , and . However, we did not find a significant correlation between bacterial diversity and estrogen. These observations will lead to a better understanding of the relationship between bone homeostasis and the microbiota in postmenopausal osteoporosis.