Turbulent Prandtl number (Prt) has a great impact on the performance of turbulence models in predicting heat transfer of supercritical fluids. Unrealistic treatment of Prt may lead to large deviations of the prediction results from experimental data under supercritical conditions. In this study, the effect of Prt on heat transfer of supercritical water was extensively studied by using shear stress transport (SST) k–ω turbulence model, and the results suggested that using the existing Prt models would lead to failures in predicting the heat transfer characteristics of supercritical water under deteriorated heat transfer (dht) conditions. A new variable Prt model was proposed with the Prt varied with pressure, turbulent viscosity ratio, and molecular Prandtl number. The new model was validated by comparing the numerical results with the corresponding experimental data, and it was found that the new variable Prt model exhibited better performance on reproducing the dht of supercritical water in vertical tubes than those of the existing Prt models.