Here, the frequency mutation problem of flexible shaft-disk rotor system was studied to explore the correlation law between system parameters and frequency mutation. Firstly, the dynamic model of flexible shaft-disk rotor system was derived with the theory of rotor dynamics. The system was discretized with the finite element method and the assumed mode method, and the corresponding differential equations were derived. The correctness of the built dynamic model was verified. Then, to study abrupt change of the system’s natural frequencies, the dimensionless parameters including radius of shaft ri, outer radius of disk rD, thickness of disk hD and position of disk lD were parametrically analyzed, and equifrequency curve phenomenon for natural frequencies of flexible shaft-disc rotor system was found. It was shown that on this equifrequency curve, the system’s natural frequencies under the condition of zero rotating speed are insensitive to change of parameter rD or lD, and basically keep unchanged. Finally, Campbell diagram and modal diagram were used to further reveal the difference of effects of parameters rD and lD changes, respectively on vibration characteristics of flexible shaft-disk rotor system.