A detailed multi-zone thermodynamic simulation has been developed for the direct-injection diesel engine combustion process. For the purpose of predicting heterogeneous-type combustion systems, the model explores the formation of pre-ignition radicals, start of combustion (SOC), and eventual heat release (including oxidation of incomplete combustion products). These mechanisms are predicted based on the conceptual model of Dec, which provides complete descriptions for the evolution of a reacting diesel fuel jet. Six zones are developed to take into account the surrounding bulk gas, liquid-phase fuel, vapor-phase fuel, pre-ignition mixing, fuel-rich combustion products, as well as the diffusion flame combustion products. The predicted cylinder pressures and heat release rates are compared to the experimental measurements from a 4.5 l, inline four-cylinder John Deere diesel engine for a range of operating conditions with different engine speeds and loads, and exhaust gas recirculation levels. Specifically, the engine possessed a compression ratio of 16.6, and had a bore and stroke of 106 and 127 mm. The results suggest that the simulation is not only valid under the conventional combustion condition, but also successfully predicts combustion processes under high exhaust gas recirculation level conditions. In particular, the detailed thermodynamics and characteristics with respect to the combustion process are investigated under different exhaust gas recirculation levels.