The natural circulation loop (NCL) plays an important role in nuclear reactor especially in the event of pump failure, while studies related to supercritical carbon dioxide (SCO2) under natural circulation loop is very scarce. In this study, the heat transfer characteristics of supercritical carbon dioxide based on natural circulation system are investigated both experimentally and numerically. The normal heat transfer and heat transfer deterioration (HTD) are observed in experiments. The effects of inlet temperature, heat flux, operating pressure and mass flow rate on the heat transfer characteristics of SCO2 in the natural circulation loop are analyzed based on the experimental data. The mechanism of supercritical carbon dioxide HTD is analyzed by numerical simulation. It is found that the HTD of supercritical carbon dioxide is mainly caused by the effect of buoyancy force due to density variation. The dimensionless density can reflect variation of HTD comprehensively. Through mechanism analysis, the buoyancy force varies the turbulent structure of the internal flow field and reduces the generation of turbulent kinetic energy. Gradually, the heat transfer efficiency is reduced due to the laminarization of a turbulent flow, which leads to the occurrence of HTD phenomenon. The research results have certain guiding significance for theoretical research, and prediction correlation of HTD of supercritical carbon dioxide also establishes the theoretical basis and benefits the application of supercritical carbon dioxide natural circulation loop in the Fourth Generation Nuclear Reactor.