Objective To explore the diagnostic value of dynamic multi-detector computer tomography (MDCT) with volume helical shuttle (VHS) technique in children with congenital heart disease (CHD) combined with tracheomalacia. Methods We retrospectively analyzed the imaging and clinical data of 26 patients (16 males, 10 females) with CHD who underwent both MDCT with VHS technique and fiber bronchoscope between Oct. 2014 and Aug. 2016. According to the Results of fiber bronchoscope, the patients were divided into tracheomalacia (n=7) and non-tracheomalacia (n=19) groups. The intracardiac structures and the anatomy of the great arteries were demonstrated by maximum intensity projection (MIP) and volume render (VR) reconstruction. The patterns of the tracheobronchial tree were demonstrated using minimum intensity projection (MinIP) reconstruction.The Mimics 17.0 software was employed to automatically segment the CT images of different respiratory phases of each patient and to measure the cross sectional area of the airway. According to the golden-standard of fiber bronchoscopic findings and operative results, we calculated the diagnostic accuracy of VHS for CHD and the sensitivity, specificity and accuracy for tracheomalacia. Results Compared with non-tracheomalacia group, the patients in tracheomalacia group showed significantly greater cross-sectional area change of the trachea (34.23%-74.95% vs 13.73%-78.87%, P=0.02). The diagnostic sensitivity, specificity and accuracy of VHS technique for tracheomalacia were 85.71%(6/7), 84.21%(16/19) and 84.62%(22/26), respectively. VHS showed accuracies of 100%(12/12) and 91.67%(11/12) in diagnosing extracardiac and intracardiac defects, respectively. Conclusion Dynamic MDCT with VHS technique can provide a one-step diagnosis of tracheomalacia with CHD in children.