Our previous research investigated the sensitivity of combustion phasing to intake temperature and injection timing during the transition from homogeneous charge compression ignition (HCCI) to partially premixed combustion (PPC) fuelled with generic gasoline. The results directed particular attention to the relationship between intake temperature and combustion phasing which reflected the changing of stratification level with the injection timing. To confirm its applicability with the use of different fuels, and to investigate the effect of fuel properties on stratification formation, primary reference fuels (PRF) were tested using the same method: a start of injection sweep from -180° to -20° after top dead center with constant combustion phasing by tuning the intake temperature. The present results are further developed compared with those of our previous work, which were based on generic gasoline. In the present work, a three-stage fuel-air stratification development process was observed during the transition from HCCI to PPC. Moreover, a transition stage was observed between the HCCI and PPC stages. Within this transition stage, both the combustion and emission characteristics deteriorated. The allocation of this transition area was mainly determined by the geometric design of the fuel injector and combustion chamber. Some differences in charge stratification were observed between the PRF and gasoline. The NOx emissions of the PRF were comparable to those of gasoline. However, the NOx emissions surged during the transition stage, indicating that the PRF combustion was probably more stratified. The soot emissions from PRF and gasoline were both much higher in the PPC than the HCCI mode, though the PRF produced much less soot than did gasoline in the PPC mode.