To explore the effect of vidian neurectomy and selective vidian neurectomy in the treatment of moderate and severe persistent allergic rhinitis (AR). A total of 60 patients with moderate-to-severe persistent AR treated in Zhejiang Provincial Hospital of Integrated Traditional Chinese and Western Medicine from June 2018 to June 2020 were selected, including 28 males and 32 females. A total of 40 cases in the observation group were subjected to vidianneurectomy, while, 20 cases in the control group underwent selective vidianneurectomy. Patients in the two groups were followed up at 6 months, 1 year, and 2 years, respectively, and evaluated according to AR diagnostic and efficacy assessment criteria. Four symptoms of sneezing, clear runny nose, nasal congestion, and nasal itching were scored as efficacy indices before and at 6 months, 1 year, and 2 years after surgery. The regression of the lower turbinate swelling after surgery was assessed by nasal endoscopy or sinus CT. Postoperative tear secretion was followed up in both groups, and patients with dry eyes were counted in combination with ocular symptoms. SPSS 19.0 software was used to statistically analyze the data before and after the surgery and between the two groups. The preoperative, 6-month, 1-year, and 2-year postoperative inferior turbinate signs were (2.73±0.45), (1.20±0.41), (1.25±0.49) and (1.30±0.56) points in the observation group and (2.75±0.44), (1.45±0.69), (1.75±0.72) and (1.90±0.85) points in the control group, respectively, with a statistically significant difference in the between-subjects effect test between the two groups (=8.28, <0.05), indicating a more durable surgical effect in the observation group. The total effective rate at 2 years after surgery was 95.0% (38/40) in the observation group and 50% (10/20) in the control group. The difference between the two groups by Fisher's exact test was statistically significant. No dry eye patient was found in either group at a 1.5-year postoperative follow-up. Both vidianneurectomy and selective vidianneurectomy have good recent treatment effects, vidianneurectomy has better long-term curative effects than selective vidianneurectomy.