Background: pulmonary atresia (PA) is a group of heterogeneous complex congenital heart disease which need more than one study modality to get correct diagnoses. This study aims to investigate the diagnostic power of low-dose dual-source computed tomography (DSCT) for all intracardiac and extracardiac anomalies in patients with PA compared with transthoracic echocardiography (TTE).Materials and methods: This retrospective study enrolled 73 patients and divided them into three groups according to their main diagnosis. All associated malformation and clinical information, including treatments, were recorded and compared among the three groups. The diagnostic power of DSCT and TTE on all associated anomalies were compared. The surgical index (McGoon ratio, pulmonary arterials index (PAI), and total neopulmonary arterial index) and radiation dose were calculated on the basis of DSCT.Results: Of the patients, 29, 29, and 15 were divide into the groups of PA with ventricular septal defect (VSD), PA with VSD and major aortopulmonary collateral arteries, and PA with other major malformations, respectively. Consequently, 178, 144, and 12 intracardiac, extracardiac, and other major anomalies were diagnosed, respectively. Moreover, DSCT showed a better diagnostic performance in extracardiac anomalies (137 vs 100, p = 0.000), whereas TTE could diagnose intracardiac anomalies better (158 vs 134, p = 0.001). The McGoon ratio, PAI, and treatment methods were significantly different among the three groups (p = 0.027, p = 0.035, and p = 0.041, respectively).Conclusion: More than one imaging modality should be used to make a correct diagnosis when clinically suspecting PA. DSCT is superior to TTE in diagnosing extracardiac anomalies and could be used to roughly calculate surgical indices to optimize treatment strategy.