The CS model coil cryogenic system had experienced many transient disturbances because of AC losses and quenches during the coil experiment. The cryogenic system adopted a forced-flow circulating loop to refrigerate the coil system by supercritical helium, and it was observed how the disturbances affected the refrigeration loop. When the disturbance occurred, the loop pressure suddenly increased such as an adiabatic-compression phenomenon in an incompressible fluid loop. Thermal disturbance, however, generated and grew in the coil-cooling channels and moved with the coolant velocity. Through the observation of disturbance, a cryogenic-system operation method that could control the influence because of disturbance was developed. The method functioned by 25 times of the transient disturbance and did not cause the cryogenic system to stop.