Objective To observe the effects of buccal acupuncture therapy and body acupuncture therapy on plasma metabolomites of rheumatoid arthritis rabbits model; To search for the metabolites related to the mechanism of buccal acupuncture and body acupuncture. Methods Sixteen rabbits were made into rheumatoid arthritis models by complete freund's adjuvant before the treatment. The buccal acupuncture group was treated by buccal acupuncture on the knee acupoint; 13 mm × 0.32 mm needle straight 0.2–0.5 mm, twist the main points of stimulation 15 s, once a day. The body acupuncture group was treated by body acupuncture on the Xiyan and Zusanli acupoints; with 13 mm × 0.32 mm needle straight 2–3 mm, every 5 min each time, twisting needle method, 100 times/min for 15 s, once a day. After the continuous treatment for 5 days, UPLC-QTOF/MS was applied to test metabolite from the plasma sample of all groups. Similarity analysis, hierarchical cluster analysis (HCA), principal component analysis (PCA), orthogonal partial least squares-discriminant analysis (OPLS-DA) were applied in this research; meanwhile load analysis method was used to identify the meaningful metabolites. Results The similarity analysis, HCA and PCA all showed the significant difference of endogenous metabolites in plasma samples among the buccal acupuncture group, the body acupuncture, the model group and the blank group. The 4 groups of different plasma sample metabolite were completely separated in three dimensions by OPLS-DA and all the samples were gathered respectively. The load analysis indicated that there were 19 kinds of endogenous metabolites which showed the significant differences between buccal acupuncture group and model group, and also happened between the body acupuncture group and the model group; N-cetyl-L-phenylalanine and 2-phenyl propionate in metabolism of phenylalanine and tyrosine decreased significantly in the buccal acupuncture group while significantly increased in the body acupuncture group. Conclusion There are relative similarity on the mechanism of treating rheumatoid arthritis between buccal acupuncture and body acupuncture. However, N-acetyl-L-phenylalanine and 2-phenyl propionate, as the main potential biomarkers of the difference, indicate that the dissimilarity can be significant.