The present study investigated the in-cylinder combustion for low octane 70 primary reference fuel (PRF70) by the method of the flame index during the transition from homogeneous charge compression ignition (HCCI) combustion to partially premixed combustion (PPC). Full cycle engine simulations were performed using CONVERGE™, coupled with chemical kinetics. Good agreements between the simulations and experiments were achieved at HCCI and PPC combustion modes. The fully premixed HCCI mode was achieved at the earliest injection timing of −180 CAD aTDC with the combustion temperature below 1600 K, where the formation of soot and NOx can be successfully avoided. For the injection timing of −100 CAD aTDC, the premixed charge compression ignition (PCCI) was achieved where the premixed combustion clouds were mainly distributed in the piston top-land zone and were surrounded by the diffused combustion that occurs in the piston bowl and the periphery of piston top. Less premixed flames were formed in piston top and surrounded by more diffusion mixtures at PPC mode. The in-cylinder HO evolution profile displayed two bumps which were distributed in low temperature zone and high temperature zone respectively. The spatial and temporal evolution of HO is very similar to the distribution of premixed flames.