Objective: To explore the mechanism of moxibustion for rheumatoid arthritis (RA) by observing the metabolite changes in urine using liquid chromatography-mass spectrometry (LC-MS)-based metabolomic analysis. Methods: Twenty-four rats were randomly divided into a control group, a model group, and a moxibustion group. Rats in the model and moxibustion groups were established as collagen-induced arthritis (CIA) models. The control and model groups did not receive any intervention; rats in the moxibustion group received moxibustion at Shenshu (BL23) and Zusanli (ST36). After three weeks of intervention, ankle joint, serum, and urine samples were collected for pathological examinations and metabolomic tests. Results: After moxibustion treatment, the CIA rats showed increased body mass, reduced swelling of the hind paws and arthritis score, decreased serum cytokine levels, and improved histopathological evaluation of the ankle joint. Twenty-four significantly altered metabolites were found, mainly involved in alanine metabolism, taurine and hypotaurine metabolism, tricarboxylic acid cycle, phenylalanine metabolism, tyrosine metabolism, and primary bile acid biosynthesis. These metabolites may serve as potential biomarkers for RA. Conclusion: Moxibustion can effectively resist inflammation in CIA rats. The potential biomarkers and the abnormal metabolic pathways of RA can be identified by LC-MS-based metabolomics. Metabolomics may be an effective way to explain the mechanism of moxibustion in treating RA.