Background Bronchiolitis is a common airway infection in young children. Hemodynamically significant congenital heart disease (CHD) predicts a more complicated course. However, the role of airway anomalies remains unknown. Methods We retrospectively reviewed the records of patients under 2 years old, diagnosed with CHD, and admitted between January 2011 and December 2013, before the palivizumab era. Records of bronchiolitis admissions were also extracted. Patients were grouped according to CHD condition and airway anomalies. Results A total of 230 patients with CHD were enrolled. A total of 180 (78%) and 71 (31%) patients had hemodynamically significant CHD and airway anomalies, respectively. A total of 52 (22.6%) patients were admitted for bronchiolitis 78 times. Among them, 33 (63.5%) had hemodynamically significant CHD, and 28 (53.8%) had airway anomalies. In patients with bronchiolitis admissions, the mean ventilator use, intensive care unit stay, and hospital stay were 1.08, 4.08, and 15.19 days, respectively. When compared, the mean hospital stay for bronchiolitis patients with airway anomalies was significantly longer than that of those without airway anomalies (19.8 vs. 9.9 days, p = 0.008). When further divided the patients by the presence hemodynamic significance, patients with hemodynamically significant CHD and airway anomaly had longer hospital stay than those who had neither. (21.7 vs. 8.3 days, p = 0.004) Airway anomaly was a significant risk factor for longer hospital stay in linear regression model (p = 0.007). Conclusions Airway anomalies are common in children with CHD and are associated with longer hospital stays on bronchiolitis admission. An active survey for airway anomalies and adequate prophylaxis for bronchiolitis infection might be important in the care of children with CHD associated with airway anomalies.