Background The anomalous origin of the right coronary artery (RCA) from the left coronary artery sinus (AORL) is one of the abnormal origins of the coronary arteries. Most of these issues rarely have any effects on human health, but some individuals may exhibit symptoms, such as myocardial ischemia or even sudden death. Recently, researchers have investigated the AORL through clinical cases, but studies based on computational fluid dynamics (CFD) have rarely been reported. In this study, the hemodynamic changes between the normal origin of the RCA and the AORL are compared based on numerical simulation results. Methods Realistic three-dimensional (3D) models of the 16 normal right coronary arteries and 26 abnormal origins of the RCAs were constructed, respectively. The blood flow was numerically simulated using the ANSYS software. This study used a one-way fluid-solid coupling finite element model, wherein the blood is assumed to be an incompressible Newtonian fluid, and the vessel is assumed to be made of an isotropic linear elastic material. Results The cross-sectional area differences between the inlet of the normal group and that of the abnormal group were significant (P < 0.0001). Moreover, there were significant differences in the volumetric flow (P = 0.0001) and pressure (P = 0.0002). Positive correlation exists for the ratio of the cross-sectional area of the RCA to the inlet area of the ascending aorta (AAO), and the ratio of the inlet volumetric flow of the RCA to the volumetric flow of the AAO, in the normal (P = 0.0001,r = 0.8178) and abnormal (P = 0.0033,r = 0.6107) groups. Conclusion This study demonstrates that the cross-sectional area of the AORL inlet may cause ischemia symptoms. The results obtained by this study may contribute to the further understanding of the clinical symptoms of the AORL based on the hemodynamics.