Parameters identification of cracked rotors has been gaining importance in recent years, but it is still a great challenge to determine the crack parameters including crack location, depth, and angle for operating rotors. This work proposes a new method to identify crack parameters in a rotor-bearing system based on a Kriging surrogate model and an improved nondominated sorting genetic algorithm-III (NSGA-III). A rotor-bearing system with a breathing crack is established by the finite element method and the superharmonic components are used as index to detect the cracks, the Kriging surrogate model between crack parameters and the superharmonic component amplitudes of the vibration response for rotors are constructed, and an improved NSGA-III is proposed to obtain the optimal crack parameters. Numerical experiments show that the proposed method can identify the crack location, depth, and angle accurately and efficiently for operating rotors.