Coal plays a leading role in  current China′s primary energy consumption. Clean and efficient conversion of coal is an important part of building a clean, low-carbon, safe and efficient energy system in China. The critical information of electronic structure and geometric configuration from transition states which is difficult to be measured by experimental methods can be investigated by quantum chemistry method. The molecular release, migration and transformation process of coal thermochemical conversion are revealed from the micro level to provide theoretical guidance for the clean utilization of coal. The characteristics and functions of density functional theory (DFT)-based methods in the study of coal structure and reactivity were investigated and the application of thermochemical conversion mechanism in coal combustion pollutant removal, gasification, pyrolysis and liquefaction was summarized. The removal mechanism of NOx and heavymetal pollutants in coal combustion, the promotion mechanism of coal char gasification reaction, the removal mechanism of oxygen-containing functional groups in coal pyrolysis and the hydrogen transfer mechanism in coal liquefaction were discussed. DFT methods can effectively reveal the properties of a certain aspect of coal and the characteristics shown in the reaction, but there is still a lack of comprehensive understanding of the molecular structure of coal. With the further improvement of relevant theoretical understanding, DFT methods will provide guidance for more clean utilization and conversion technology of coal through its advantages in micro-mechanism research.