The direct-injection-premixed charge compression ignition–based combustion process with a high exhaust gas recirculation ratio and early injection timing is simulated using a Reynolds-averaged Navier–Stokes–based commercial computational fluid dynamics code with a nonhomogeneous mixture auto-ignition combustion model. In addition, the formation processes of nitrogen oxide (NO), carbon monoxide (CO), and unburnt hydrocarbon are calculated. The calculation results are compared with the experimental data. According to the calculation results, the formation processes of NO, CO, and hydrocarbon are discussed in relation to the spray development and ignition point. Furthermore, the combustion process of two-stage injection is also calculated. The result shows that the combustion process is described well by this model except in the case where auto-ignition occurs in the squish area. Additionally, the relationship between the combustion process and the mixture distribution is clarified. The main origins of the unburnt hydrocarbon and CO emissions are located in the center region of the combustion chamber, where the mixture becomes excessively lean and low in temperature.