To observe the effect of herb-partitioned moxibustion (HPM) for primary dysmenorrhea. Six hundred and forty patients were randomized assigned (1∶1) to HPM group and control group. Duration of treatment was 3 months with 3 month follow-up. The primary outcome was pain relief measured by visual analogue scale (VAS). The second outcomes were Cox Menstrual Symptom Scale (CMSS), menstrual pain duration and frequency of analgesics usage. The exploratory outcome included quality of life, RESULTS: After the 3-month treatment and follow-ups, the pain intensity measured by VAS was significantly reduced in both groups compared with baseline (P < 0.05), and it was significantly decreased in HPM group than that of control group (P < 0.001). The higher proportion of participants in the HPM group had a decrease of at least 50% in VAS at the end of treatment, as compared with the control group (P < 0.001). At the 3rd and 6th month, the menstrual pain duration, CMSS score and frequency of analgesics usage in HPM group were significantly lower than those of control group (P < 0.05). After 3 month treatment and follow-ups,the scores of physical, psychological, social and environmental domains were significantly increased than baseline in both groups (P < 0.05), and the sores of physical, psychological and environmental domains were significantly higher in HPM group than those of control group (P < 0.05) . Herb-partitioned moxibustion reduced menstrual pain and improved quality of life, these were sustained for up to 3 months after treatment. Further research is needed to understand long term effect and the mechanism of the intervention.