Backgrounds: Allergic rhinitis (AR) is highly prevalent worldwide, but its treatment is poor. Myofascial trigger point (MTrP) injections have been effectively used for the management of many chronic painful diseases. Latent MTrPs (we called Qi points, QiPs) could be with autonomic nerve phenomena. Little is known about the correlation between QiPs and AR. Therefore, we proposed the hypothesis that QiPs might play a role in the pathophysiological mechanisms of AR. The current study was designed to investigate the efficacy and safety of QiPs injection therapy for AR. Methods: Sixty-five patients who suffered from moderate to severe AR were enrolled in this study. All patients received QiPs injection therapy in the referred facial and cervical muscles only once. The total nasal symptom score (TNSS) and side-effects was collected during the following 24 weeks. Results: The patients reported that their nasal and eye symptoms were significantly improved compared to those previously reported. The TNSS in the 15 minutes after treatment was significantly lower compared with the score before treatment, and the effect was maintained for at least 24 weeks. No obvious side effects were recorded during the treatment or the follow-up period. Conclusions: QiPs injection therapy provided long-term clinical efficacy with few adverse events in moderate to severe AR patients. QiPs inflammation in the facial and cervical regions, which causes nasal mucous oversecretion by regulating upper cervical sympathetic nerve ganglion and sphenopalatine ganglion activity, might play a novel role in the etiology of AR.