To observe the clinical efficacy of electroacupuncture (EA) with different frequencies in treating migraine. Ninety patients with migraine were divided into a low frequency electroacupuncture (LF-EA) group, a high frequency electroacupuncture (HF-EA) group and a variable frequency electroacupuncture (VF-EA) group by the random number table method. Shuaigu (GB 8), Hegu (LI 4), Waiguan (TE 5), Taichong (LR 3), Taiyang (EX-HN 5), Fengchi (GB 20) and Ashi points were selected for all three groups. After achieving needling sensation (Deqi), the LF-EA group received 2 Hz continuous wave EA stimulation; the HF-EA group received 100 Hz continuous wave EA stimulation, and the VF-EA group received 2 Hz/100 Hz sparse-dense wave EA stimulation. The EA stimulation lasted for 30 min in all the three groups, once a day, 10 times as a course, and the clinical efficacy was evaluated after 2 consecutive courses of treatment. After treatment, the total effective rates in the LF-EA group, HF-EA group and VF-EA group were 77.7%, 83.3% and 93.3%, respectively. The difference in total effective rate between the LF-EA and HF-EA groups was not statistically significant (P>0.05), but the total effective rate was significantly higher in the VF-EA group than in the LF-EA and HF-EA groups (both P 0.05), while the score was significantly lower in the VF-EA group than in the LF-EA and HF-EA groups (both P<0.01). VF-EA (2 Hz/100 Hz), compared with LF-EA (2 Hz) and HF-EA (100 Hz), shows superior clinical efficacy in treating migraine.