In order to realize the cleanliness of coal chemical production process, high-end target products and transformation of the industry under the goal of "double carbon", the endowment characteristics of coal molecules are used as the starting point to enhance the value of its fine conversion products. Mass spectrometry (MS) can clearly analyze the structural characteristics of coal molecules at the molecular level. This paper reviewed the research progress in coal molecules and mild conversion of coals using collision induced dissociation, a MS method. The progress of research related to the structure of coal molecules was reviewed. Determining the distribution of heteroatoms on aromatic nuclei and lipid chains allows the evaluation of the differences in reactivity of heteroatoms at different positions. The study of mass spectrometry methods in coal molecular structure profiling provides methodological guidance for understanding coal molecular structure units, monitoring heteroatom reaction pathways, and optimizing catalysts and reaction systems.