Environmental pollution from transportation means and natural resource degradation are the top concern globally. According to statistics, NOx and PM emissions from vehicles account for 70% of total emissions in urban areas. Therefore, finding solutions to reduce NOx and PM emissions is necessary. Changing the engine's internal combustion method is considered promising and influential among the known solutions. One of the research directions is a combustion engine using the Premixed Charge Compression Ignition (PCCI) method combined with biofuels to improve the mixture formation and combustion process, reducing NOx and PM emissions. Therefore, this study presents the mechanism of the formation of PM and NOx emissions in the traditional combustion and the low-temperature combustion process of internal combustion engines. Besides, the theoretical basis of flame spread during combustion is also introduced. The key feature of this research is that it has modeled the combustion process in diesel engines under the PCCI modes. This was accomplished using blends of waste cooking oil (WCO)-based biodiesel and diesel fuel, as well as the ANSYS Fluent software. The results showed that PCCI combustion using B20 fuel can significantly reduce NOx and PM emissions, although HC and CO emissions tend to increase, and thermal efficiency tends to decrease. In further studies, different modes of the PCCI combustion process should be thoroughly examined so that this process can be implemented in practice to reduce pollutant emissions.