An experiment was conducted to investigate the effect of charge stratification on the combustion phasing in a single cylinder, heavy duty (HD) compression ignition (CI) engine. To do this the start of injection (SOI) was changed from -180° after top dead centre (ATDC) to near top dead centre (TDC) during which CA50 (the crank angle at which 50% of the fuel energy is released) was kept constant by changing the intake temperature. At each SOI, the response of CA50 to a slight increase or decrease of either intake temperature or SOI were also investigated. Afterwards, the experiment was repeated with a different intake oxygen concentration. The results show that, for the whole SOI period, the required intake temperature to keep constant CA50 has a “spoon” shape with the handle on the -180° side. Depending on the required intake temperature, the whole SOI period is divided into five zones: the injection against intake valve closing zone, the classical Homogeneous Charge Compression Ignition (HCCI) zone, the top-land/crevice effect zone, the stratification effect zone, and the ignition delay effect zone. From the sensitivity study, it is found that a higher intake temperature always leads to an earlier CA50 for the whole SOI period, while an earlier SOI can either result in an earlier or a later CA50, depending on how this variation of SOI affects the mixing process. When SOI is within the last three zones, CA50 is sensitive to the changes of both the intake temperature and SOI. But relatively, the sensitivity of CA50 to SOI is higher. When the exhaust gas recirculation (EGR) is not used, CA50 becomes more sensitive to SOI and less sensitive to the intake temperature. The THC, CO, and NOx emissions increase and the combustion efficiency decreases especially during the top-land/crevice effect zone.