OBJECTIVE To evaluate the efficacy of endoscopic vidian neurectomy in the management of moderate-severe persistent allergic rhinitis, and to explore its possible mechanism. METHODS One hundred and ninety-one patients with moderate-severe persistent allergic rhinitis were divided into three groups: endoscopic vidian neurectomy was carried out in 71 patients (group A), partial inferior turbinectomy and/or septal-plasty in 39 patients (group B), and 81 patients were as control (group C). The life quality was assessed at 6 month, 1 year and 3 years after operation using rhinoconjunctivitis quality of life questionnaire (RQLQ) and visual analogue scale (VAS). RESULTS Among 191 cases, one hundred and forty-five cases had complete follow-up documents. The average score of RQLQ and VAS score (x(-) ± s) were significantly decreased at the time of 6 months (0.84 ± 0.41, 2.55 ± 1.57), 1 year (0.91 ± 0.43, 2.63 ± 1.71) and 3 years (1.03 ± 0.46, 2.81 ± 1.75) after endoscopic vidian neurectomy than scores before operation (2.25 ± 0.49, 7.34 ± 1.11), F = 115.45, 133.09, respectively, P < 0.001, and also significantly lower than scores in patients in group B or control group at the same period after treatment. By patient's self-evaluation, the ratio of greatly-improved, improved and not-improved was respectively, 65.5% (38 cases), 24.1% (14 cases), 10.4% (6 cases), and significantly higher in patients in group A than in patients in group B (U = 237.0, P < 0.001) and group C (U = 246.0, P < 0.001). There was no severe complication in all patients observed. CONCLUSIONS Endoscopic vidian neurectomy is an effective and safe technique in the management of moderate-severe persistent allergic rhinitis.