In-cylinder visualization, combustion stratification, and engine-out particulate matter (PM) emissions were investigated in an optical engine fueled with Haltermann straight-run naphtha fuel and corresponding surrogate fuel. The combustion mode was transited from homogeneous charge compression ignition (HCCI) to conventional compression ignition (CI) via partially premixed combustion (PPC). Single injection strategy with the change of start of injection (SOI) from early to late injections was employed. The high-speed color camera was used to capture the in-cylinder combustion images. The combustion stratification was analyzed based on the natural luminosity of the combustion images. The regulated emission of unburned hydrocarbon (UHC), carbon monoxide (CO) and nitrogen oxides (NO) were measured to evaluate the combustion efficiency together with the in-cylinder rate of heat release. Soot mass concentration was measured and linked with the combustion stratification and the integrated red channel intensity of the high-speed images for the soot emissions. The nucleation nanoscale particle number and the particle size distribution were sampled to understand the effect of combustion mode switch.