The effect of cathode airflow variation on the dynamics of a fuel cell gas turbine hybrid system was evaluated using a cyber-physical emulator. The coupling between cathode airflow and other parameters, such as turbine speed or pressure, was analyzed comparing the results at fixed and variable speed. In particular, attention was focused on fuel cell temperatures and gradients: cathode airflow, which is generally employed for thermal management of the stack, was varied by manipulating a cold-air bypass. A significant difference was observed in the two cases in terms of turbine inlet, exhaust gas, cathode inlet, and average cell temperatures. When the turbine speed was held constant, a change in cathode airflow resulted in a strong variation in cathode inlet temperature, while average cell temperature was not significantly affected. The opposite behavior was observed at variable speed. The system dynamics were analyzed in detail in order to explain this difference. Open-loop response was analyzed in this work for its essential role in system identification. However, a significant difference was observed between fixed and variable speed cases, because of the high coupling between turbine speed and cathode airflow. These results can give a helpful insight of system dynamics and control requirements. Cold-air valve bypass position also showed a strong effect on surge margin and pressure dynamics in both cases.