In a former research, the sensitivity of combustion phasing to intake temperature and injection timing during the transition from HCCI to PPC were investigated, fueling with generic gasoline. While digging into the results, special interest was drawn into the relationship between the intake temperature and combustion phasing since it was believed that it properly revealed the changing of stratification level with the injection timing. To confirm its applicability on different fuels also investigate the effect of fuel properties on the formation of stratification, primary reference fuels (PRF) was tested with the same method: a start of injection sweep from -180° to -20° aTDC (after top dead center) with the combustion phasing kept constant by tuning the intake temperature. The results were compared with the former results of gasoline, and the previous conclusions were further developed. A three-stage fuel-air stratification development process, from HCCI to PPC, was observed. And a transition stage was seen between the HCCI stage and PPC stage. Within this transition stage, the combustion and emission characteristics both deteriorated. The allocation of this transition area was mainly decided by the geometrical design of the injector and combustion chamber. Some differences in charge stratification were observed between the PRF and gasoline. The NOx emission of PRF is comparable to gasoline. However, the NOx emission bump during the transition stage revealed that the combustion of PRF was probably more stratified. The soot emissions of PRF and gasoline were both much higher in PPC mode than in HCCI mode. And the PRF got much less soot in PPC mode than gasoline.