ABSTRACT: Osteoporosis represents a significant health challenge, particularly in postmenopausal women. While traditional medicine offers potential solutions, the mechanisms underlying their efficacy remain elusive. This study demonstrates the bone-protective properties of Guilu Erxian gel decoction (GEX), a traditional medicine prepared from tortoise plastron, antler, and herbs, by elucidating its impact on gut microbiota and associated metabolites. Using an ovariectomized mouse model of postmenopausal osteoporosis, we demonstrate that GEX consumption significantly reduces key osteoporotic markers, including low bone mineral density, compromised trabecular microstructure, and reduced biomechanical strength. GEX intake profoundly reshapes the gut microbiome, enriching beneficial bacteria crucial for fatty acid metabolism and mineral absorption. Gut microbiota transplantation from GEX-fed mice to ovariectomized recipients reversed probiotic bacterial abundance, particularly Bifidobacterium and Akkermansia. This intervention effectively alleviated ovariectomy-induced colon inflammation, trimethylamine N-oxide (TMAO) overproduction, and osteoporosis progression. Excessive TMAO promotes osteoclastogenic differentiation in macrophages in vitro. Using μCT imaging, biomechanical testing, histological staining, and 16S rRNA sequencing, we provide compelling evidence for the complex therapeutic effects of GEX, including mitigation of osteoclast overburden, reduction of marrow adiposis, suppression of RANKL overproduction, and preservation of colon goblet cell mucin. This study demonstrates the interplay between gut microbiota, its metabolite TMAO, and bone health, offering new insights into the mechanism of action of GEX. Our findings not only validate the bone-protective potential of this traditional medicine but also open new avenues for developing microbiome-based strategies to combat osteoporosis.