Partially premixed compression ignition combustion is one of the low temperature combustion techniques which is being actively investigated. This approach provides a significant reduction of both soot and NOx emissions. Comparing to the homogeneous charge compression ignition mode, PPCI combustion provides better control on ignition timing and noise reduction through air-fuel mixture stratification which lowers heat release rate compared to other advanced combustion modes. In this work, CFD simulations were conducted for a low and a high air-fuel mixture stratification cases on a light-duty optical engine operating in PPCI mode. Such conditions for PRF70 as fuel were experimentally achieved by injection timing and spray targeting at similar thermodynamic conditions. After validating the computed results of cylinder pressure, apparent heat release rate, and OH* spatial distributions, differences in engine thermal load and mixture fraction distributions at first stage and second stage ignition were compared. Assuming similar second stage ignition timing which is provided by intake air heating, experimental and simulation results reveal that the time between first and second stage ignition shortens and combustion phases to the main stage ignition faster in the high stratification case. Using flame structure diagrams, this was attributed to availability of a larger range of mixture fractions with higher reactivity. Creating optimum air-fuel stratification then can be considered as a useful and additional controlling parameter for a PPCI engine combustion phasing and subsequent emission formation.