Objective To detect the influence of heating coagulation of the middle meningeal artery on c-fos expression in the trigeminal caudalis nucleus in migraine rats triggered by nitroglycerin. Methods Forty-eight female Wistar rats were randomly assigned to four groups, the isotonic saline group (group A), the nitroglycerin group (group B), the operation group (group C), and the sham operation group (group D), with 12 subjects in each group and each group was subdivided into another two equal groups after successfully constructing the animal model. C-fos expression in the trigeminal caudalis nucleus was detected by means of RT-PCR and Western blot respectively. Results Injection of 10mg/kg nitroglycerin was able to trigger the animal model of migraine as evidenced by the appearances of a series of symptoms, such as frequently head scratching, climbing the cage and red ear. The scores of these behaviors for each group were respectively 2.33±0.74, 39.57±5.44, 37.87±4.68, 15.6±3.30. At the same time, c-fos expressionsin the trigeminal caudalis nucleu in group B, group C, or group D was significantly increased compared with that of group A (P<0.05). More importantly, c-fos expression in the trigeminal caudalis nucleus in group D was much lower than that in group B and group C (P<0.05), but there was no statistical difference between group B and group C (P>0.05). Conclusions Results show that heat coagulation of the middle meningeal artery may attenuate head complaint of rats induced by nitroglycerin, and it is concluded that the middle meningeal artery plays a primary role in the pathophysiology of the rat migraine model triggered by nitroglycerin and the efficacy may play a part in decreasing c-fos expression and containing activation of neurons in the trigeminal caudalis nucleus .