Objective To study the clinical value of echocardiography (Echo) and multi-slice spiral CT (MSCTA) in the diagnosis of complex congenital heart disease in children. Methods Seventy-nine cases of children with pathologically confirmed complex congenital heart disease in the hospital were selected as the research object who received MSCTA and Echo diagnosis at the same time. The rates of detection, missed diagnosis and misdiagnosis of two kinds of detection methods were compared with pathologic diagnosis results. The sensitivity and false negative rate were calculated. Results Among the 45 patients with abnormalities of intracardiac structure, there were 29 cases of patients detected by MSCTA, 16 cases of missed diagnosis (aortic regurgitation in 5 parts, single atrium in 3 parts, patent foramen ovale in 1 part, pulmonary atresia in 2 parts and atrioventricular valve regurgitation in 5 parts). There were 42 cases detected by Echo with 3 cases of missed diagnosis (single atrium in 2 parts, patent foramen ovale in 1 part). Among the 208 cases of abnormality outside the heart, there were 195 cases detected by MSCTA with 10 cases missed diagnosis and 3 cases of misdiagnosis; There were 137 cases detected by Echo among whom there were 60 cases of missed diagnosis and 11 cases of misdiagnosis. Most of the types of missed diagnosis were pulmonary artery abnormal broadening and right-sided aortic arch which were respectively in 18 and 15 parts; For MSCTA diagnosis, the sensitivity of abnormalities of intracardiac structure was 64.44% and the false negative rate was 35.55% while for Echo diagnosis respectively were 93.33% and 6.67%. The sensitivity of Echo was significantly higher than that of MSCTA (P<0.05). The sensitivity of MSCTA in diagnosis of abnormality of extracardiac structure was 93.75% and false negative rate was 6.25% whle of Echo diagnosis respectively were 65.87% and 34.13%. The sensitivity of MSCTA was significantly higher than that of Echo (P<0.05). Conclusion Echocardiography and CT were effective ways to diagnose complex congenital heart disease in children. The sensitivity of echocardiography in detecting abnormalities of intracardiac structure is higher, but the accuracy of detecting abnormalities of extracardiac structure is lower than that of 64 slice spiral CT. It is recommended that the two combined to improve the detection rate of complex congenital heart disease in children.