Supercritical fluid based heat transfer loop (NCL) has become a hot topic in energy conversion systems. In such systems, supercritical natural convection stability and heat transfer conditions are crucial for design and safe operation. In the present study, numerical simulations were performed to investigate the influences of heater orientations on the performance of supercritical CO2 based circulation loops. The numerical model is based on Navier-Stokes equations with supercritical turbulence effects considered. It is found that the heat source location has significant influence on the flow pattern and system heat transfer. Vertical heating cases are found stable in a wide range of heat flux conditions due to the changes of buoyancy force torques across the NCLs, while horizontal heating cases show transition heat flux and oscillations are still seen. However, the influence of heat source location is less significant on the heat transfer characteristics. The effect of cooler heat transfer is found of special importance for the heat transfer and system stability behaviors. The NCL flow and heat transfer correlations are also compared in this study, and it is recommended that more numerical and experimental studies be made in the future.