Objective To explore the long-term clinical efficacy, safety, and impact on the growth and development of children with congenital choanal atresia treated with mucosal flap fabrication combined with fully degradable sinus drug stent under nasal endoscope.Methods A retrospective analysis was conducted on 28 children diagnosed with congenital choanal atresia from January 2018 to February 2021 at Beijing Children’s Hospital Affiliated to Capital Medical University. All patients were treated with nasal endoscopic mucosal flap technology combined with a fully degradable sinus drug stent system, with the indicator line of the stent system set at the external nose to self shedding. Regwlar follow up after surgery. The indicator line shedding time, the stent full absorption time, and the improvement of nasal congestion were recorded. Electronic nasopharyngoscopy was performed to observe whether the nasal cavity structure was abnormal, the formation of the posterior nostril, the rate of restenosis, and the incidence of complications after surgery. The growth and development of the childen were evaluated according to the National Health Commission’s “Growth Standards for Children Under 7 Years” WS/T423-2022.Results One week after discharge, telephone consultations were conducted and the nasal congestion had disappeared in all patients. The average shedding time of the indicator line was 30.55±4.75 days, and all patients were followed up for 2 to 5 years. Short-term (within one year) follow-up revealed no complications related to stent placement in all patients. Long-term (more than one year) follow-up showed stable shaping effect of the posterior nostril without restenosis. Except for 3 cases with syndrome, the height and weight curves of the other children 2 years after surgery were within the normal range of peers, and no effect of local nasal hormone application was found on the growth and development of the children.Conclusions The preparation of mucosal flap and the expansion of bony choanae are the key to ensure the long-term efficacy of pediatric choanal atresia surgery.The application of fully degradable sinus drug stent after surgery is the key to avoid short-term local complications. Setting up stent system indicator lines is a safe auxiliary method. No long-term effect on the growth and development of children due to the persistent low-dose hormone released by the stent system in the nasal cavity can be observed in clinic.