Background: Three-dimensional (3D) printing is promising in medical applications, especially presurgical planning and the simulation of congenital heart disease (CHD). Thus, it is clinically important to generate highly accurate 3D-printed models in replicating cardiac anatomy and defects. The present study aimed to investigate the accuracy of the 3D-printed CHD model by comparing them with computed tomography (CT) images and standard tessellation language (STL) files. Methods: Three models were printed, comprising different CHD pathologies, including the tetralogy of Fallot (ToF), ventricular septal defect (VSD) and double-outlet right-ventricle (DORV). The ten anatomical locations were measured in each comparison. Pearson’s correlation coefficient, Bland–Altman analysis and intra-class correlation coefficient (ICC) determined the model accuracy. Results: All measurements with three printed models showed a strong correlation (r = 0.99) and excellent reliability (ICC = 0.97) when compared to original CT images, CT images of the 3D-printed models, STL files and 3D-printed CHD models. Conclusion: This study demonstrated the high accuracy of 3D-printed heart models with excellent correlation and reliability when compared to multiple source data. Further investigation into 3D printing in CHD should focus on the clinical value and the benefits to patients.