Objective. To explore the efficacy and mechanism of primary dysmenorrhea patients were treated with herb-partitioned moxibustion through metabonomics. Methods. 20 patients with primary dysmenorrhea were randomized into two groups, separately treated with herb-partitioned moxibustion at CV8 (shenque) and acupuncture at SP6 (sanyinjiao). After three menstrual cycles' treatment, the intensity of menstrual pain using VAS and the changes of metabolites of plasma using LC-MS were observed. Results. The VAS of two groups decreased with different descending range. Herb-partitioned moxibustion upregulated 20α-dihydroprogesterone, pregnenolone, prostaglandin E2 and γ-aminobutyric acid and downregulated the content of estrone and prostaglandin H2, while acupuncture upregulated pregnenolone and 20α-dihydroprogesterone and downregulated 2-methoxyestradiol-3-methylether, 15-hydroxyeicosatrienoic acid and 6-keto-prostaglandin. Discussion. It was effective in relieving the abdominal pain by these two therapies. Herb-partitioned moxibustion is superior to acupuncture for primary dysmenorrhea, which could be related to regulating the endocrine hormone.