A comprehensive description of the protein should include its structure, thermodynamics, and kinetic properties. The recent rise of cryogenic electron microscopy (cryo-EM) provides new opportunities for the thermodynamic and kinetic research of proteins. There have been some researches in which cryo-EM is used not only to resolve the high-resolution structure of proteins but also to analyze the conformational distribution of proteins to infer their thermodynamic properties based on data processing methods. However, whether cryo-EM can be used to directly quantify the kinetics of proteins is still unclear. In this work, an ideal protein system, cyanobacterial circadian clock protein, is selected to explore the potential of cryo-EM used to analyze the non-equilibrium process of proteins. Previous research has illustrated that cryoelectron microscope can be used to infer the thermodynamic information about the KaiC protein such as the inter-subunit interaction within the hexamers. Herein, we extend the equilibrium Ising model of KaiC hexamers to a non-equilibrium statistical physics model, revealing the properties of the non-equilibrium process of KaiC hexamers. According to the non-equilibrium model and previous biochemical research, we find that the intrinsic properties of KaiC protein allow its non-equilibrium conformational distribution to be measured by cryo-EM.