Toward higher efficiency and lower emissions, modern direct injection (DI) engines employ various injection strategies. This leads to more complex in-cylinder spray evaporation and combustion processes, requiring more comprehensive modeling approaches. In this study, an extended flamelet model is developed to describe DI engine combustion over a wide range of injection timings. A key feature of the model is to fully incorporate the interaction between spray evaporation and gas-phase combustion. Additional source terms representing the effect of evaporation were incorporated in the flamelet equation solved in the reactive space. A simple test problem demonstrated that the new formulation successfully accounts for the history of the spray evaporation. The extended formulation was implemented into a multidimensional computational fluid dynamics (CFD) code KIVA3v for full cycle engine simulation. The modeling results were successfully validated against available experimental data obtained from a rapid compression facility.