Objective To explore the diagnostic value of ultrasound and CT in complex congenital heart disease. Methods 86 patients with complex congenital heart disease were selected as the study subjects in our hospital from May 2012 to May 2017, who were confirmed by surgical pathology and preoperative ultrasonography and CT examination were performed. To have a comparative analysis of surgical diagnosis and ultrasonography, CT and the combination of the two diagnostic results, respectively. Results This group of patients confirmed by surgery, a total of 217 heart deformities, the structure of the coronary artery was 66, and the structure of the atrioventricular junction was 112, and the large vascular structure of the heart was 39. Ultrasound detected 196 heart deformities, the diagnostic accuracy rate was 90.32%. CT examination detected 197, the diagnostic accuracy rate was 90.78%; the combined use of ultrasound and CT combined examination detected 211, the diagnostic accuracy rate was 97.24%, the accuracy of the combined diagnosis was significantly higher than that of ultrasound or CT alone, the difference was statistically different (P<0.01). Conclusion Ultrasound and CT in the diagnosis of complex congenital heart disease have their own advantages and disadvantages, the two ways combined can achieve complementary advantages, significantly improve the diagnostic accuracy, at the same time, the inspection method is not invasive, costless, and have high clinical application value.