Objective To analyze the clinical effect of highly selective branches neurotomy of vidian nerve in the treatment of vasomotor rhinitis. Methods Sixty patients with vasomotor rhinitis who were treated in People′s Hospital of Yichun City from June 2019 to March 2020 were selected and divided into the control group and the observation group according to the random number table method, with 30 cases in each group. The patients of the control group were treated with inferior turbinate ablation and nasal septum correction. The patients of the observation group were treated with highly selective branches neurotomy of vidian nerve. Patients of both groups were followed up for 12 months. Before the operation (T0), 1 month after operation (T1), 3 months after operation (T2), 6 months after operation (T3) and 12 months after operation (T4), the symptoms, signs score and visual analog scale (VAS) scoreand the postoperative complications of the two groups were compared. Results There were statistically significant differences in the time, intergroup and interaction of the scores of symptoms and signs between the two groups (P<0.05). Further pairwise comparison, there were no statistically significant differences in the scores of symptoms and signs between the two groups at T0 (P>0.05). The scores of symptoms and signs of the two groups at T1 were higher than those at T2, the scores of symptoms and signs at T2 were higher than those at T3, and the scores of symptoms and signs at T3 were higher than those at T4, and the differences were statistically significant (P<0.05). At T1, T2, T3 and T4, the scores of symptoms and signs in the observation group were lower than those in the control group, and the differences were statistically significant (P<0.05). There were statistically significant differences in the time, intergroup and interaction of the VAS score between the two groups (P<0.05). Further pairwise comparison, there was no statistically significant difference in VAS score at T0 between the two groups (P>0.05). VAS scores of the two groups at T0 were higher than those at T1, VAS scores at T1 were higher than those at T2, VAS scores at T2 were higher than those at T3, VAS scores at T3 were higher than those at T4, and the differences were statistically significant (P<0.05). VAS scores of the observation group were lower than those of the control group at T1, T2, T3 and T4, and the differences were statistically significant (P<0.05). The total incidence of postoperative complications in the observation group was lower than that in the control group, and the difference was statistically significant (P<0.05). Conclusion In patients with vasomotor rhinitis, the treatment effect of highly selective branches neurotomy of vidian nerve is better, which can adjust the clinical symptoms and signs of patients, alleviate pain, and has better safety.