Coal-based cryptocrystalline graphite is an intermediate phase formed during the transformation of highly metamorphic anthracite into crystalline graphite. In order to explore the relationship between the graphitization degree of coal-based cryptocrystalline graphite and its physical properties from macromolecular structure to provide a theoretical basis for industrial application, samples were tested by X-ray diffraction, electrochemistry, and thermal conductivity and compared with standard graphite (SG) and artificial thermal simulation graphitized samples. The results show that with the increase of graphitization degree and the growth of microcrystalline structure, the electrical impedance of cryptocrystalline graphite decreases, the conductivity increases, the specific capacity of initial discharge increases, and the thermal conductivity increases, which gradually approach the electrical and thermal properties of crystalline graphite. The linear equations between impedance and L a and L c are y = −0.42x + 70.44 and y = −1.87x + 70.62, and the correlation coefficients are 0.93 and 0.88. The linear equations between thermal conductivity and the horizontal extension length (L a ) and vertical stacking thickness (L c ) are y = 0.09x + 1.36 and y = 0.4x + 0.76, the correlation coefficients are 0.82 and 0.84., and the reduction of microcrystalline parameters d 002 and the increase of L a and L c lead to a direct improvement of physical properties. Artificial thermal simulation samples also show the same regularity, but their physical properties are lower than those of natural evolution samples. Short-term high-temperature simulation is different from long-term magma heat and pressure, and the growth of graphite microcrystals is more complete under long-term geological conditions, resulting in better physical properties.