The coal fragmentation and resulting particle size distribution (PSD) have significant influences on the physical and chemical properties, which play a crucial role in coal conversion and utilization processes. In this paper, a comprehensive comminution theory of superfine pulverized coal was proposed, in combination of particle fracture mechanisms, fractal dimension analysis, and energy laws of comminution. The subtle crystalline changes of aggregate structures as a result of the coal comminution were validated through synchrotron-based high-resolution X-ray diffraction, and the distribution patterns of sub micrometer aggregate clusters were identified according to the fractal fragmentation theory. Finally, a novel energy dissipation assumption is proposed on the basis of the molecular sliding mechanism, which is suitable for the evaluation of energy consumption of the comminution-induced sub-micrometer particles. The results here can improve the interpretation and modeling of coal macromolecular networks and offer a new way for predicting the PSD of grinding products. The findings from this work provide some new insights into the phenomenon of limit fineness of mechanical comminution from a molecular level perspective, which is helpful for the development of fragmentation methodology and equipment in the field of ultrafine grinding.