Purpose: Anomalous pulmonary venous connection (APVC) is a rare congenital heart anatomical deformity. 64-slice spiral CT angiography (64-SSCTA) has been widely used in cardiovascular examination. However, research on 64-SSCTA in APVC is not much. This paper aimed to study the diagnostic advantage of 64-SSCTA and three-dimensional reconstruction in patients with APVC. Methods: From 2009 to 2015, 83 segments of pulmonary vein of anomalous drainage in 22 patients confirmed by surgery were analyzed. All patients underwent transthoracic echocardiography (TTE) at 48 hours before 64-SSCTA enhanced scan, followed by three-dimensional reconstruction in the workstation. 64-SSCTA and TTE results were compared with surgery results respectively. Results: The difference between 64-SSCTA and the surgery results was not statistically significant (P = 0.155), but the difference between TTE and the surgery results was statistically significant (P = 0.001). 64-SSCTA (Pearson test r = 0.892, Kappa value = 0.714, accuracy was 97.6%) was strongly related to the surgery results, and the TTE (Pearson test r = 0.347, Kappa value = 0.537, accuracy was 86.7%) was slightly related to the surgery results. Conclusion: In the diagnosis of ectopic drainage pulmonary vein of complex congenital heart disease, 64-SSCTA and 3D reconstruction have good consistency with operation control (Kappa value = 0.714, P<0.001), could be used as a good noninvasive examination method in the preoperative assessment of the deformity.