Objective To analyze the diagnostic value of ultrasound (US) and magnetic resonance imaging (MRI) in fetal congenital heart disease (FCDH). Methods The US and MRI data of 100 cases of puerperas with suspected FCDH from January 2017 to January 2018 in our hospital were analyzed. The pathological examination results were used as the gold standard to evaluate the application value of US and MRI in fetal heart malformations. Results In 100 cases of puerperas, 91 cases were fetuses delivered and 9 cases were with induced labour, and 87 cases of fetuses with heart malformations were detected by ultrasonic screening and fetal autopsy with the detection rate of 87%, including 11 cases (11%) of single atrium/ventricular malformation, 13 (13%) of atrial/ventricular dysplasia, 15 (15%) of double outlet ventricle, 12 (12%) of tetralogy of fallot, 9 cases (9%) of transposition of the great vessels, 18 cases (18%) of valvular heart malformation and 9 cases (9%) of others (P>0.05). There was no significant difference in the diagnostic coincidence rate in the diagnosis of single atrium, atrial/ventricular dysplasia, double outlet ventricle, tetralogy of fallot, and great vessels transposition by pure US, MRI and combined diagnosis (P>0.05), and there were significant differences in the diagnostic coincidence rate of valvular heart malformation and others (P<0.05). The sensitivity, specificity and accuracy were 81.61%, 61.54% and 79.00% by pure US, and were 71.26%, 53.85% and 69.00% by pure MRI, and were 95.40%, 61.54% and 91.00% by US combined with MRI. Conclusion US is superior to MRI in judging the direction of blood flow and the movement of heart valves. MRI can effectively show the direction of large blood vessels. US is superior in indicating the location of large blood vessels and peripheral organs. It can make up for the deficiency of US. US combined MR can effectively improve the detection rate and accuracy of FCDH. Worthy of clinical promotion.