Objective To explore the diagnosis value of MSCT for complex congenital heart disease in children. Methods Selected from 2014 to 2015 in our hospital surgery diagnosis of children with complex congenital heart disease in 27 cases, All patients were examined by multi-slice spiral CT and ultrasound (ultrasound) in 1 month before surgery. The difference of the two patients was confirmed by the two methods. Results A total of 27 patients with heart malformation in 41, the diagnostic rate of MSCT for (39, 95.12%) and US (40, diagnosis rate 97.56%) there was no significant difference (χ2 =0.346, P=0.556). There are a large part of patients with vascular malformation in 35, the diagnosis rate of MSCT (34, 97.14%) higher than the diagnosis rate of US (27, 77.14%), and the difference was statistically significant (χ2 =4.590, P=0.032). The total number of cardiac and vascular connections was 35, and the diagnostic rate of MSCT (34, 97.14%) was higher than that of US (25, 71.42%), and the difference was statistically significant (χ2 =8.737, P=0.003); All patients were cardiac malformation in 111, the diagnosis rate of MSCT (107, 96.40%) higher than the diagnosis rate of US (92, 82.88%), and the difference was statistically significant (χ2 =10.913, P=0.001). Conclusion The diagnostic accuracy of multi-slice spiral CT in children with complex congenital heart disease is higher than that of echocardiography.