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To investigate the effect of vidian trunk neurectomy and selective vidian branch neurectomy on treating moderate-to-severe persistent allergic rhinitis. Sixty patients with moderate-to-severe persistent allergic rhinitis treated at Zhejiang Hospital of Integrative Medicine participated in this study from June 2018 to June 2020. The patients in the observation group (n = 40) underwent a vidian trunk neurectomy. The patients in the control group (n = 20) underwent a vidian branch neurectomy. The patients in both groups were followed up after 6 months, 1 year, and 2 years of surgery. The efficacy was evaluated based on the AR diagnostic and the efficacy assessment criteria. The 4 symptoms of sneezing, runny nose, nasal congestion, and nasal itch were scored as efficacy indices before and 6 months, 1 year, and 2 years after surgery. Nasal endoscopy or sinus CT was performed to assess the postoperative inferior turbinate swelling. The postoperative tear secretion was followed up in both groups, and patients with dry eyes were counted in combination with ocular symptoms. The data recorded before and after surgery and between the 2 groups were analyzed statistically. The observation group had signs of 2.73 ± 0.452 before surgery, 1.20 ± 0.405 6 months after surgery, 1.25 ± 0.494 1 year after surgery, and 1.30 ± 0.564 2 years after surgery. The control group had signs of 2.75 ± 0.444 before surgery, 1.45 ± 0.686 6 months after surgery, 1.75 ± 0.716 1 year after surgery, and 1.90 ± 0.852 2 years after surgery. The between-subjects effect test between the groups showed an overall significant difference (P .05). The overall effective rate 2 years postoperatively was 38/40 (95.0%) in the observation group and 10/20 (50%) in the control group. Fisher's exact test showed a significant difference between the groups. No patient in either group had dry eyes 1.5 years after surgery. Both vidian trunk neurectomy and selective vidian branch neurectomy have good immediate therapeutic effects, and vidian trunk neurectomy has higher long-term efficacy than selective vidian branch neurectomy.