Due to small footprint and high efficiency, a Supercritical CO2 (S-CO2) power cycle is considered to be one of the promising next-generation power cycles. Although S-CO2 is reported as a powerful cleaning agent, the performance of a power system operating with S-CO2 will also inevitably degrade over time. Previous researchers have shown that turbomachinery deterioration could be a major subject regarding the system performance degradation. Nevertheless, no quantitative evaluation has yet been made so far. In this study, the impact of the performance degradation of the S-CO2 turbomachinery on the overall performance of the system is analyzed quantitatively. The concept of Health Parameter is used to simulate turbomachinery degradation. To quantify the impact, an S-CO2 direct-cycle small modular reactor is selected as a target system. A transient analysis platform is built using a nuclear system safety analysis code and the deep neural network (DNN)-based S-CO2 turbomachinery off-design performance model. System dynamics are evaluated for primary frequency control ability and secondary load-following capability. Results show that the control problems during the transient state can occur when the output fluctuations are large and the performance degradation is severe. It has been confirmed that even control failures of the PID controllers can occur. Therefore, the performance degradation of turbomachinery must be monitored and considered, for an operation strategy for S-CO2 systems.