The cyber physical system is widely applied to industrial Internet of Things system and its security determines the safety of the industrial IoT system. This paper proposes a multilevel fine fingerprint authentication method for the security protection of key operating equipment. Firstly, Because of the acquired signals, the mathematical representation models are established separately, including the self-encoding model on the basis of the multiorder moment features and the multi-scale representation model based on the wavelet. Secondly, the multigranularity features of the time domain and frequency domain are extracted respectively based on the real-time data's self-encoding representation and multiscale representation. Then, the extracted features of different granularities can be built into the image representation based on the time-frequency fusion portrait. Based on the images of different granularities and the legitimate image library, a multiscale matching authentication method is established. Finally, simulation experiments show that the proposed method is effective.