This work aims to study the effect of fuel inhomogeneity on the ignition process and subsequent combustion in a compression ignition Partially Premixed Combustion (PPC) engine using a primary reference fuel (PRF) in low load conditions. Five cases with injection timings ranging from the start of injection (SOI) at -70 crank angle degrees (CAD) to -17 CAD have been studied numerically and experimentally in a heavy duty (HD) piston bowl geometry. Intake temperature is adjusted to keep the combustion phasing constant. Three dimensional numerical simulations are performed in a closed cycle sector domain using the Reynolds Averaged Navier-Stokes (RANS) formulation with k-ϵ turbulence closure and direct coupling of finite rate chemistry. The results are compared with engine experiments. The predicted trends in required intake temperature and auto-ignition location for a constant combustion phasing are consistent with experiments. The simulations show that the auto-ignition is critically dependent on both fuel and temperature stratification. The ignition occurs in fuel-lean regions but the mixing of the fuel with the cylinder gas and the cylinder gas temperature stratification (prior to injection) determines the ignition location. A higher heat release rate is observed in the later injection cases, which is attributed to the higher equivalence ratio of the mixture inside the bowl. Negative temperature coefficient (NTC) heat release behaviour of the studied fuel plays a role in shortening the ignition wave propagation but the impact of the effect varies among the injection cases. A sensitivity study of combustion efficiency with regard to the intake temperature is performed on two of the cases (SOI of -30 CAD and of -63 CAD). While the combustion phasing is slower and correctly predicted in the simulations of the advanced injection cases the combustion efficiency is found to be very sensitive to the intake temperature. This is attributed to the high sensitivity of the ignition delay time to equivalence ratio and temperature.