Objective: The aim of this study was to investigate the efficacy of endoscopic selective vidian neurectomy in the treatment of severe persistent allergic rhinitis (AR) combined with chronic rhinosinusitis (CRS) with nasal polyps (ARwCRSwNP). Methods: One hundred thirty patients with moderate to severe persistent ARwCRSwNP were enrolled at Xuanwu Hospital, Capital Medical University, from September 2015 to September 2017. Patients were divided into 2 groups. Sixty-one patients (the control group) underwent conventional surgical treatment for CRS with nasal polyps and received conservative treatment for AR. Sixty-nine patients (the experimental group) received conventional surgical treatment for CRS with nasal polyps plus endoscopic selective vidian neurectomy with amputation of the posterior nasal nerve and pharyngeal branch of the vidian nerve. Clinical parameters, including visual analog scale (VAS) score, Lund-Kennedy endoscopic mucosal morphology score, and Lund-Mackay sinus computed tomography (CT) scan lesion range score, were used to analyze and evaluate the preoperative and postoperative data. Comparisons were based on patient scores, and preoperative and postoperative scores obtained at 6, 12, and 24 months were analyzed. Results: The experimental group had higher therapeutic efficacy in nasal obstruction, nasal itching, rhinorrhea, sneezing, and general symptoms than the control group (p < 0.05). No complications such as tear-secretion disorder or atrophic rhinitis occurred in the experimental group, and no significant difference in complications incidence was observed between the 2 groups (p > 0.05). Conclusion: Endoscopic selective vidian neurectomy is an effective and safe technique for the management of moderate to severe persistent ARwCRSwNP.