In the last decade, supercritical carbon dioxide power cycle has attracted worldwide attention. The characteristics of flow instability are critical for the design and safe operation of supercritical carbon dioxide power cycle. In the present paper, theoretical and experimental study was carried out to investigate the characteristics of flow instabilities in supercritical carbon dioxide natural circulation loop. A new explanation of the mechanism of flow oscillation in supercritical carbon dioxide natural circulation has been put forward. It found that the pressure fluctuation, which resulted from the variation of heat transfer mode, might be amplified under the condition of appropriate non-dimensional pressure drop in supercritical fluids natural circulation loop. Effects of typical thermal parameters on flow instabilities of supercritical carbon dioxide natural circulation were discussed in detail. Results showed that, for supercritical fluids natural circulation system, an increase in the system pressure and the local resistance coefficient in the cold section, and a decrease in the local resistance coefficient in the hot section could enhance the system stability.