Injection flow dynamics plays a significant role in fuel spray; this process controls the fuel–air mixing, which in turn is critical for the combustion and emissions process in diesel engine. In the current study, an integrated spray, combustion, and emission numerical model is developed for diesel engine computations based on the general transport equation analysis (GTEA) code. The model is first applied to predict the effect of turbulence inside the nozzle, which is considered by the submodel of hybrid breakup model on diesel spray process. The results indicate that turbulence term enhances the rate of breakup, resulting in more new droplets and smaller droplet sizes, leading to high evaporation rate with more evaporated mass. The model is also applied to simulate combustion and soot formation process of diesel. The effects of ambient density, ambient temperature, oxygen concentration and reaction mechanism on ignition delay, flame lift-off length, and soot formation are analyzed and discussed. The results show that although higher ambient density and temperature reduce the ignition delay and cause the flame stabilization location to move upstream, this is not helpful for fuel–air mixing because it increases the soot level in the fuel jet. While higher oxygen concentration has negative effects on soot formation. In addition, the model is employed to simulate the combustion and emission characteristics of a low-temperature combustion engine. The overall agreement between the measurements and predictions of in-cylinder pressure, heat release, and emission characteristics are satisfactory.