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It is great significance to understand the mechanism of heat transfer deterioration of supercritical CO2 for heat exchanger design and safe operation in the supercritical CO2 Brayton cycle. Three-dimensional steady-state numerical simulation was performed to investigate the behavior of supercritical CO2 heat transfer in heated vertical up-flow tube with inner diameter di = 10 mm and heated length Lh = 2000 mm. Based on the characteristics of inverted-annular film boiling at subcritical pressure, the heat transfer model of supercritical CO2 flowing in the heated vertical tube was established in this paper. The mechanisms of heat transfer deterioration (HTD) and heat transfer recovery (HTR) for supercritical CO2 were discussed. Numerical results demonstrate that HTD is affected by multiple factors, such as the thickness and property of vapor-like film near the wall, the turbulence intensity near the interface between liquid-like and vapor-like, and in the liquid-like core region as well as the distribution of radial velocity vector. Among the above factors, the change of turbulent kinetic energy caused by the buoyancy effect seems to be a more important contributor to HTD and HTR. Furthermore, the influences of heat flux and mass flux on the distribution of wall temperature were analyzed, respectively. The reasons for the difference in wall temperature at different heat fluxes and mass fluxes were explained by capturing detailed thermal physical properties and turbulence fields. The present investigation can provide valuable information for the design optimization and safe operation of a supercritical CO2 heat exchanger.