To investigate the flow characteristics of supercritical carbon dioxide (sCO2) during natural cycling under heating and cooling conditions, this study establishes a three-dimensional rectangular circular loop system and employs computational fluid dynamics (CFD) methods to analyze the steady-state and transient properties. The results indicate that the heating and cooling sections are influenced by wall heating and cooling, resulting in local flow oscillations. Consequently, the horizontal velocity exhibits an “M”-shaped distribution. Under different pressure levels, the mass flow rate initially increases with heating power, reaching a peak at 7.5 MPa, 8 MPa, and 9 MPa. The peak value decreases with higher cooling temperatures and is also lower under the same heating power conditions. Further analysis of the flow instability at 7.5 MPa and 9 MPa pressures reveals that flow instability is primarily caused by density changes in the heating section. The instability is more likely to occur at lower heating power levels due to insufficient heating power.