Partially premixed combustion (PPC) is an operating mode that lies between the conventional compression ignition (CI) mode and homogeneous charge compression ignition (HCCI) mode. The combustion in this mixed mode is complex as it is neither diffusion-controlled (CI mode) nor governed solely by chemical kinetics (HCCI mode). In this study, CFD simulations were performed to evaluate flame index, which distinguishes between zones having a premixed flame and non-premixed flame. Experiments performed in the optical engine supplied data to validate the model. In order to realize PPC, the start of injection (SOI) was fixed at −40 CAD (aTDC) so that a required ignition delay is created to premix air/fuel mixture. The reference operating point was selected to be with 3 bar IMEP and 1200 rpm. Naphtha with a RON of 77 and its corresponding PRF surrogate were tested. The simulations captured the general trends observed in the experiments well. The flame index was noted to be an indicator to evaluate and quantify the in-cylinder combustion development under PPC engine operating condition. The evolution of premixed flames shows the same two-stage ignition behavior as the rate of heat release. Premixed flames are surrounded by the non-premixed fuel/air mixtures and distribute in the piston top-land region as isolated clouds. The proportion of premixed flames increases from low temperature heat release (LTHR) region first and decreases in negative temperature coefficient (NTC) region then increases to high temperature heat release (HTHR) region at PPC mode.