The experimental in-cylinder combustion process was compared with the numerical simualtion for naphtha fuel under conventional compression ignition (CI) and partially premixed combustion (PPC) conditions. The start of injection timing (SOI) with the single injection strategy was changed from late of −10 CAD aTDC to early of −40 CAD aTDC. The three-dimensional full cycle engine combustion simulation was performed coupling with gas phase chemical kinetics by the CFD code CONVERGE™. The flame index was used for evaluating the combustion evolution of premixed flame and diffusion flame. The results show that the flame index could be used as an indicator for in-cylinder homogeneity evaluation. Hydroperoxyl shows a similar distribution with the premixed combustion. Formaldehyde could be used as an indicator for low temperature combustion.