Background: To investigate the therapeutic effectiveness and safety of endoscopic dacryocystorhinostomy (EN-DCR) to treat congenital nasolacrimal canal dysplasia (CNCD). Methods: Forty children (50 eyes) with congenital nasolacrimal duct obstruction (CNLDO) and lacrimal bony dysplasia, including 8 children with bony atresia (10 eyes) and 32 with bony stenosis (40 eyes), were recruited in this retrospective study. Standardized EN-DCR was performed in all cases. The postoperative observations included relief of symptoms, fluorescein dye disappearance test (FDDT), syringing of lacrimal passages and anastomotic patency under nasal endoscopy. Patients were followed up for 8-18 months. Results: Standardized EN-DCR surgery had a success (cure and improvement) rate of 100%, including a cure rate of 82% and an improvement rate of 18%. The cure rate among 40 cases of bony nasolacrimal duct stenosis was 82.5%, while that of 10 cases of bony nasolacrimal duct atresia was 80%. Statistical analysis showed that nether the receipt of other treatments before surgery nor the type of bony nasolacrimal duct dysplasia affected the cure rate. No significant complications were observed during postoperative follow-up except for four cases (4 eyes) that suffered middle turbinate and nasal mucosal adhesion and two cases with sinusitis. Conclusions: CNCD is a type of CNLDO that does not respond to conservative and conventional treatment. EN-DCR represents a safe and effective treatment for children with CNCD. In addition, the combination of EN-DCR with lacrimal CT scanning provides advantages over traditional lacrimal surgery in that it has a high success rate with a low incidence of complications.