Objective To investigate and analyze the application value of transthoracic echocardiography (TTE) and dual-source computed tomography (DSCT) in the preoperative diagnosis of children with congenital heart disease (CHD). Methods The clinical data of 70 cases of children with congenital heart disease (CHD) treated in our hospital from July 2013 to July 2016 were retrospectively analyzed. All subjects were examined with TTE and DSCT before operation. Referred to the results of pathological diagnosis, the sensitivity and accuracy were compared between the two diagnostic methods. Results Among 70 cases of children, there were a total of 176 malformations, and 156 cases was detected by TTE (88.64%) and 146 cases was detected by DSCT (82.95%) (P>0.05). There were a total of 93 cases of cardiac malformations, and the diagnostic sensitivity and accuracy of TTE were significantly higher than those of DSCT [(96.77% and 98.30%) vs. 968.82% and 83.52%)] (P<0.05). There were a total of 30 heart-large blood vessels connecting part of malformations, and diagnostic sensitivity and accuracy of both TTE and DSCT were 100.00% (P>0.05). There were 53 large blood vessel malformations, and the diagnostic sensitivity and accuracy of TTE were significantly lower than those of DSCT [(66.04% and 89.20%) vs. (98.11% and 99.43%)] (P<0.05). Conclusion TTE and DSCT have their own advantages and disadvantages. The sensitivity and accuracy of TTE are high in detecting partial cardiac malformations while the sensitivity and accuracy of DSCT are high in detecting partial malformation of large vessels.