In this study, Partially Premixed Combustion (PPC) on a modified heavy-duty diesel engine was realized by hybrid combustion control strategy with flexible fuel injection timing, injection rate pattern modulation and high ratio of exhaust gas recirculation (EGR) at different engine loads. It features with different degrees of fuel/air mixture stratifications. The very low soot emissions of the experiments called for further understanding on soot formation mechanism so that to promote the capability of prediction. A new soot model was developed with highlight in effects of surface activity on soot growth for soot formation prediction in partially premixed combustion diesel engine. According to previous results from literatures on the importance of acetylene as growth specie of PAH and soot surface growth, a gas-phase reduced kinetic model of acetylene formation was developed and integrated into the new soot model. Modified HACA mechanism proposed by Colket and Hall was applied for soot surface growth due to H-Abstraction-C2H2-Addition, which idea is accepted as core theory for soot formation mechanism. By correlation study, it was found that the activity of soot surface was affected by both mixture temperature and equivalence ratio at homogeneous combustion and equivalence ratio factor becomes more weightiness than temperature as inhomogeneity increases in diesel combustion. Therefore, a new formula of the fraction of active sites αCH was put forward in formulation of local mixture temperature and inhomogeneity for the soot surface growth sub-model. When the mixture was quite homogeneous, lowered combustion temperature was the main factor for reduced soot formation due to the lowered specific surface growth rate, in spite of αCH increasing slightly caused by slowed decay rate of surface activity. As the inhomogeneity of the mixture was increased, more unburned hydrocarbons were produced, promoting the formation of acetylene and soot surface activity. It was the dominated reason for higher soot surface growth rate, resulted worsened engine-out soot.