The detailed flow, combustion process and emissions are studied within a In-Direct Injection (IDI) type diesel engine fueled with isooctane using a three-dimensional CFD code known as integrated CKL (CHEMKIN-KIVA-LES) solver that has been successfully developed by the authors to capture the details of turbulence flow structures and chemical kinetics. This CKL solver features three-dimensional turbulent two-phase flow and combustion with one equation k-Δ Large Eddy Simulation (LES) model for turbulence and CHEMKIN for chemical kinetics. The CKL solver was validated using the experimental data from modified KUBOTA D905 IDI type diesel engine converted to HCCI engine. Then the CKL solver is employed to study the effect of fuel injection strategies on the HCCI engine combustion process. Simulations were carried out for three cases (a) with port fuel injection assuming uniform fuel distribution within the intake port, (b) direct injection into the cylinder during intake stroke at 90 CA and (c) direct injection into the pre-chamber during the intake stroke at 90 CA. The results show that fuel injection into the intake port ahead using pre-heated air intake gives lower emissions compared to direct injection simulations. The results from direct injection show that injection at the center of the cylinder during intake stroke improves the fuel mixing and gives better thermal efficiency compared to injection in the pre-chamber. Quantitative results suggest that direct injection within the cylinder during intake stroke gives similar IMEP (Indicated Mean Effective Pressure) and thermal efficiency as port injection but slightly higher emissions. Direct fuel injection timing can be controlled to achieve optimum efficiency with lower emissions and can have direct control over the combustion process. Qualitative results are presented in terms of velocity vector fields, temperature fields, species concentration contours to understand the fuel mixing process and combustion phenomena.