Advanced oxidation processes (AOPs) have a broad range of potential applications in the treatment of emerging refractory emerging pollutants. However, due to the presence of highly reactive substances such as free radicals that are difficult to capture, it is challenging to investigate the mechanism of AOPs at the elementary reaction level. The conventional methods, such as electron spin resonance (ESR), free radical quantification, and free radical quenching, are plagued by systematic issues that have led to bottlenecks in the field of AOP studies. The development of computational chemistry theory and computer performance provides a new method to study the mechanism of AOPs through density functional theory (DFT) calculation. Due to its excellent cost–performance benefit, DFT calculations for aperiodic small molecules have become popular in the field of AOPs. In this paper, a comprehensive review is presented on the applications of DFT calculations for predicting active sites and exploring reaction selectivity and oxidant activation mechanisms. A systematic classification of methods related to molecular descriptors and transition states is provided. Furthermore, some current research issues are identified, and future development prospects and challenges are discussed.