The supercritical carbon dioxide (S-CO2) Brayton cycle efficiency increases as the compressor inlet condition approaches the critical point. However, the thermodynamic properties of CO2 vary dramatically near the critical point, and phase change is most likely to happen. Both cavitation and condensation bring about significant adverse effects on the performance of compressors. In this paper, the quantitative effects of nonequilibrium condensation and cavitation on the performance of an S-CO2 centrifugal compressor with different inlet-relative entropy values are investigated. The properties of CO2 were provided by the real-gas property table, and the nonequilibrium phase-change model was adopted. The numerical simulation method with the nonequilibrium phase-change model was validated in the Lettieri nozzle and Sandia compressor. Furthermore, simulations were carried out in a two-stage centrifugal compressor under conditions of various inlet-relative entropy values. The type of nonequilibrium phase change can be distinguished by inlet-relative entropy. Cavitation makes the choke mass flow rate decrease due to the drop in the speed of sound. Condensation mainly occurs on the leading edge of the main blade at a large mass flow rate, but cavitation occurs on the splitter. The condensation is more evenly distributed on the main blade, but the cavitation is mainly centered on the leading edge.