Understanding the change in coal structure during heat treatment is the basis of efficient and clean utilization of coal. In this study, high-resolution transmission electron microscopy (HRTEM) was used to analyse the changes in the aggregate structure and ultramicropores of Zhungdong coal samples (Xinjiang, China) that were heated from ambient temperature to 800 °C respectively. Then, the relationship between their HRTEM characteristics and the corresponding reaction activation energy were also analyzed. The results show that the length, curvature, order, layer spacing and stacking height of the aromatic layers of the coal sample vary with an increasing temperature, and are related to the activation energy of the reaction. As the temperature reaches 300 °C, the HRTEM characteristics of the heated coal samples are obviously different from those of the raw coal sample. It is shown that the length of lattice fringes is in the range of 0.3–1.15 nm which accounts for approximately 95% of the total number of fringes. The overall orientation of lattice fringes is not good, but there are two main directions. After heating, the number of naphthalenes in the coal samples decreased, while the number of larger aromatic layers increased. The distance between the aromatic layers of the coal sample decreased with an increasing stacking height, the order of the aromatic layers was enhanced, and the number of aromatic sheets with a larger curvature increased. The coal ultramicropores are mainly concentrated from 0.4 to 0.7 nm. Heat treatment reduces the total number of ultramicropores, but the maximum number of pores is increased. The non-six-membered ring and lattice defects lead to the bending of the fringes, the distribution of fatty structures affects the orientation of the fringes, and the relationship between the pore and molecular structure does not exist independently. After heat treatment, the aggregate structure and ultramicropore size of coal have a high correlation with the activation energy. The activation energy is closely related to the 0.6 nmultramicropores. However, the current experiment could not explain the underlying causes of these relationships. The aggregated state in coal is the macromolecular group formed between different aromatic structures, fat structures and other molecules, which is formed by the interaction of internal defects and pores in the molecular group. The structural differences at different temperatures therefore reflect the interaction of different macromolecules in coal.