Abstract Background Oesophageal atresia is a congenital malformation of the oesophagus and a serious malformation of the digestive system, postoperative complications include acute respiratory failure, pneumonia, anastomotic fistula, anastomotic stenosis, tracheal stenosis, gastroesophageal reflux and eosinophilic oesophagitis, anastomotic fistula is one of the important causes of postoperative death. The objective of this study is to identify the risk factors for anastomotic complications after one-stage anastomosis for oesophageal atresia. Methods A retrospective analysis was performed on the clinical data of 107 children with congenital oesophageal atresia who underwent one-stage anastomosis in our hospital from January 2013 to December 2018. Single-factor and multivariate logistic regression analyses were performed to determine the risk factors for anastomotic fistula and anastomotic stenosis. Results A total of 107 children with oesophageal atresia underwent one-stage anastomosis, and the incidence of anastomotic fistula was 26.2%. The probability of anastomotic stenosis in the long term was 52.3%, and the incidence of refractory stenosis (dilation ≥5 times) was 13.1%. Analysis of the clinical count data in the anastomotic fistula group and non-anastomotic fistula group showed that preoperative albumin (F = 4.199, P = 0.043), low birth weight (F = 7.668, P = 0.007) and long gap defects (F = 6.107, P = 0.015) were risk factors for postoperative anastomotic fistula. Further multivariate logistic regression analysis showed that low birth weight (Wald2 = 4.499, P = 0.034, OR = 2.775) and long gap defects (Wald2 = 6.769, P = 0.009, OR = 4.939) were independent risk factors for postoperative anastomotic fistula. Premature delivery (F = 5.338, P = 0.023), anastomotic fistula (F = 11.381, P = 0.001), endoscopic surgery (F = 6.343, P = 0.013), preoperative neutrophil count (F = 8.602, P = 0.004), preoperative low albumin (F = 8.410, P = 0.005), and a preoperative prognostic nutritional index < 54 (F = 5.54, P = 0.02) were risk factors for refractory anastomotic stenosis in children. Further multivariate logistic regression analysis showed that postoperative anastomotic fistula (Wald2 = 11.417, P = 0.001, OR = 8.798), endoscopic surgery (Wald2 = 9.633, P = 0.002, OR = 4.808), and a prognostic nutritional index < 54 (Wald2 = 4.540, P = 0.002, OR = 2.3798) were independent risk factors for refractory anastomotic stenosis. Conclusion Low birth weight and long gap defects are important predictors of postoperative anastomotic fistula, and the possibility of refractory anastomotic stenosis should be considered. The long-term risk of anastomotic stenosis was increased in children undergoing endoscopic surgery and in those with a preoperative prognostic nutritional index < 54.