Electroacupuncture and moxibustion are traditional Chinese medicine practices that exert therapeutic effects through stimulation of specific meridian acupoints. However, the biological basis of the therapies has been difficult to establish; thus the current practices still rely on ancient TCM references. Here, we used a rat model to study perturbations in cortex, liver, and stomach metabolome and plasma hormones following electroacupuncture or moxibustion treatment on either stomach meridian or gallbladder meridian acupoints. All treatment groups, regardless of meridian and mode of treatment, showed perturbation in cortex metabolome and increased phenylalanine, tyrosine, and branched-chain amino acids in liver. In addition, electroacupuncture was found to increase ATP in cortex, creatine, and dimethylglycine in stomach and GABA in liver. On the other hand, moxibustion increased plasma enkephalin concentration, as well as betaine and fumarate concentrations in stomach. Furthermore, we had observed meridian-specific changes including increased N-acetyl-aspartate in liver and 3-hydroxybutyrate in stomach for gallbladder meridian stimulation and increased noradrenaline concentration in blood plasma following stimulation on stomach meridian. In summary, the current findings may provide insight into the metabolic basis of electroacupuncture and moxibustion, which may contribute towards new application of acupoint stimulation.