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Rheumatoid arthritis (RA) is an autoimmune disease characterized by persistent joint inflammation. The development of rheumatoid arthritis is directly correlated with the disturbance of gut microbiome and its metabolites. RA can be effectively treated with the Danggui Sini decoction (DSD), a Traditional Chinese medicine (TCM) prescription from the Treatise on Febrile Diseases. Further research is needed to clarify the precise mechanism of DSD in the treatment of RA. In this study, 1H NMR metabonomics and 16 S rRNA gene sequencing techniques were used to clarify the intervention of DSD on CIA-induced RA. The results of 1H NMR metabolomics of feces revealed that five metabolites (alanine, glucose, taurine, betaine, and xylose) were disturbed, which could be regarded as potential biomarkers of RA. The intestinal microbiome of RA rats had changed, according to the results of 16 S rRNA gene sequencing; eight microbes (g_norank_f_Eubacterium_coprostanoligenes_group , g_Ruminococcus_torques_group , g_Dubosiell , g_Lactobacillus , g_norank_f_Desulfovibrionaceae , g_Bacteroides , g_Oscillibacter , and g_Romboutsia) occurred significantly at the genus level, and DSD significantly impacted six of them (g_Dubosiell , g_Lactobacillus , g_norank_f_Eubacterium_coprostanoligenes_group , g_Ruminococcus_torques_grou , g_Bacteroides , and g_Romboutsia). Three of them (g_norank_f_Eubacterium_ coprostanoligenes_group , g_Romboutsia , and g_Lactobacillus) were regarded as key microbiomes for DSD to treat RA, and three common metabolic pathways (taurine and hypotaurine metabolism; alanine, aspartate, and glutamate metabolism; primary bile acid biosynthesis) were discovered based on the 1H NMR metabonomics and PICRUST2 prediction of 16 S rRNA gene sequencing. Six SCFAs in feces (acetic acid, butyric acid, propionic acid, caproic acid, isobutyric acid, and valeric acid) increased significantly in RA, according to the outcomes of targeting SCFAs, while five SCFAs (acetic acid, butyric acid, propionic acid, caproic acid, and valeric acid) had decreased significantly due to DSD treatment. In conclusion, our study indicated that DSD could regulate RA's metabolic disorder by affecting intestinal microbiome and its metabolites. It also establishes a framework for future research into exploiting gut microbes therapeutic to treat RA. • Combining metabolomics and 16 Sr RNA gene sequencing to reveal the therapeutic mechanism of DSD in the RA with Cold Bi syndrome. • Five metabolites were considered as potential biomarkers concerning collagen-induced rheumatoid arthritis. • Six intestinal bacteria were considered to be the key bacteria for DSD treating RA. • Three key pathways are considered for DSD treating RA by combined analysis of metabolomics and 16 S rRNA Gene Sequencing [ABSTRACT FROM AUTHOR]