Atractylodes Rhizoma is one of two principal components in Ermiaosan, a well-known traditional Chinese medicine for the treatment of rheumatoid arthritis (RA). Atractylodes oil (AO) represents a potential alternative treatment for RA. The purpose of this study was to investigate the effect of AO in rats with Adjuvant Arthritis (AA) by exploration of changes in serum metabolites using gas chromatography-mass spectrometry (GC-MS). Foot thickness and arthritis score, ankle joint pathological structure, the concentrations of TNF-α, IL-1β, IL-6, IL-17 and the expression of MMPs in ankle joint tissue were measured as indicators of efficacy of treatment using AO. In addition, multivariate statistical analysis was used to identify differential production of metabolites and biomarkers, and to analyze metabolic pathways. The results demonstrate that administration of AO resulted in a good therapeutic effect in the AA rat model, with significantly improved joint swelling, reduced joint score, and inhibition of inflammation, synovial pannus hyperplasia, and bone and cartilage destruction. Furthermore, AO was found to exert its effect against rheumatoid arthritis principally by differentially affecting 11 metabolites and six metabolic pathways, predominantly related to abnormal amino acid metabolism, in addition to energy-related metabolic pathways. This study evaluated the capability of AO to effectively treat AA rats, providing a novel strategy for the treatment of RA.