In the pursuit of carbon peak and neutrality targets, China′s significant reliance on coal as a primary energy source requires ongoing focus on its clean and efficient utilization. Quantum chemistry, a theoretical method used to analyze microstructure and mechanisms,has played a crucial role in coal chemistry research. By providing microscopic information, quantum chemistry has facilitated the development of clean and efficient coal utilization technology. This review aimed to summarize the application of quantum chemistry in optimizingthe molecular structure of coal models, studying reaction mechanisms, and analyzing factors affecting reactions. It also highlighted the microscopic challenges encountered in coal pyrolysis, combustion, gasification, and liquefaction, includingthe migration and transformation mechanism of nitrogen during coal pyrolysis and combustion, the gasification characteristics between functional groups and CO2, thehydrogen transfer mechanism of coal liquefaction, and the mechanism of influencing factors, such as atmosphere and catalyst. Lastly, itprovided an overview of scientific challenges faced by quantum chemistry in the field of clean and efficient coal transformation, which involvedin the evolution model of coal metamorphism, the mechanism of multi-factor effect in coal reaction, the complete transformation mechanism, catalyst optimization, and innovative integration process, offering insights for the advancement and application of clean coal technology.