Objective To discuss the clinical value of CT angiography (CTA) in the diagnosis of congenital heart disease (CHD) with heterotaxis. Methods The clinical data of 64 patients with CHD complicated with heterotaxy treated in the hospital from January 2012 to May 2017 were analyzed retrospectively. The patients were selected after being confirmed by surgery and pathology, and they were examined with echocardiography and CTA. The type of CHD and the situation of heterotaxis were determined through observation of the ventricular development and heterogeneous type, the development of pulmonary artery and lung lobe, the aortic positional relationship, the locations of liver and gastral cavity in abdominal cavity and the number of spleen. The results of CTA were compared with those of surgery and echocardiography. Results With surgical results as the standard, the accurate rates of CTA and ultrasound in the diagnosis of the type of CHD were 90.63% (58/64) and 76.56% (49/64), respectively (P<0.05). The accurate rates of CTA and ultrasound in the diagnosis of heterotaxy were 91.35% (61/64) and 79.69% (51/64), respectively (P<0.05). There was no significant difference between CTA and surgery in the diagnosis of heterotaxy (P>0.05). Conclusion CTA can well display the structures of the heart, large vessels, thorax and abdomen. The clinical diagnosis of CHD and heterotaxy with CTA is superior to ultrasound. It is of great value in the evaluation of patient's condition and the development of the surgical plan.