Osteoporosis is a common bone disorder worldwide and causes bone fragility and fracture. Gut microbiota colonizes the gastrointestinal tract, and is associated with bone metabolism and osteoporosis. In our study, the alteration of gut microbiota in osteoporosis and its effects on bone metabolism were investigated. A total of 36 elderly postmenopausal osteoporotic women and 12 healthy controls were recruited, and their fecal samples were collected for 16S rRNA gene sequencing of gut microbiota on Illumina MiSeq platform. The venous blood and urine samples were also collected to determine the biochemical indexes. There was no obvious difference in Alpha diversity in the experiment group and control group, while differential Beta diversity was observed. The Partial Least Squares Discriminant Analysis (PLS-DA) model and variable importance in projection (VIP) scores showed that the osteoporotic women and healthy controls had different genera of Erysipelotrichaceae , Rothia , and Eubacterium . The metabolic function prediction of gut microbiota indicated that the experiment group had 634 unique functional categories, while the control group had 13 unique functional categories. The biochemical measurement revealed that the osteoclast activity indexes including urine N-terminal telopeptides of type I collagen (NTX), serum NTX, and serum C-terminal telopeptides of type I collagen (CTX) in the experiment group were higher than those in the control group, indicating that the osteoclast activity in osteoporotic women was increased. In addition, the correlation analysis of microbial metabolism with phenotypes showed the pathways in the significant modules of magenta, red, pink, and yellow were positively correlated with urine phosphate, urine creatinine, urine creatinine, serum calcium and other biochemical indexes. Collectively, our study identified the different genera between postmenopausal osteoporotic women and healthy controls, which might be potential targets for the treatment of osteoporosis.