Naphtha boils in the gasoline range of 40°C to 75°C with a RON of 65, showing increased resistance to auto-ignition. It is not possible to use naphtha as a drop in fuel for CI engine and therefore, it is ideal to investigate premixed combustion of naphtha. Previous studies reports the use of naphtha in CI engine under partially premixed combustion (PPC) mode, wherein the fuel injection timing and intake air temperature controls combustion. In this study, we investigate the combustion visualization and stratification of surrogate fuel in PPC mode. The composition of naphtha surrogate is 2-methyl butane (0.21% mol), 2-methyl hexane (0.07% mol), n-pentane (0.6% mol), n-heptane (0.07% mol) and toluene (0.05% mol). Investigation of surrogate fuel in engine expands on the previous studies on surrogate fuel formation for naphtha. Based on the experimental outcome, start of injection (SOI) was found to be inversely correlated with combustion phasing during early injection timings. However, both SOI and intake air temperature controls the combustion phasing at PPC conditions. The combustion video, captured by a high speed camera, is processed and stratification analysis is performed for naphtha and its surrogate. The intensity of the combustion images plotted as a function of polar angle (θ) represent seven peak, representing the combustion clouds. Stratification analysis performed in this regard show an increased stratification for naphtha, while combustion turns homogenous when intake air is diluted by nitrogen. The combustion images are also correlated with engine out emissions such as soot concentration, NOX, HC and CO. Surrogate fuel and naphtha show decreased emissions of HC, CO and soot than that of diesel, while NOX emission is higher.