Supercritical carbon dioxide (sCO2) is a promising working medium for coal-fired power plants, high-temperature solar power systems, nuclear reactor systems, and fuel cells owing to its high efficiency and inertness. In these cases, the sCO2 is in a round tube under high temperature and pressure, far from the pseudo-critical point. Here, the thermophysical properties of sCO2 changes, resulting in large prediction errors. In this study, a conjugate heat transfer model with the k-ε turbulent model was created to analyze the tube performance of the sCO2, and the effects of turbulent Prandtl number (Prt) on the sCO2 turbulent flow with high heat flux were examined through experimental and numerical investigations. Prt had a considerable effect on the performance of the sCO2 turbulent flow far from the pseudo-critical point. The mean relative errors of the inner wall temperature and convective heat transfer coefficient were reduced by approximately 13% and 27%, respectively, when Prt was decreased from 1 to 0.55. For the sCO2 turbulent flow with a high heat flux, constant Prt values of 0.55–0.6 were applicable. The findings afford key insights for the development of sCO2 turbulent flow with high heat flux.