Simulation is performed for a diesel engine in the partial homogeneous charge compression ignition (pHCCI) mode with split injections. The spatially integrated CMC model involves an additional heat loss term for the conditional enthalpy and the evaporation source terms for the mean mixture fraction variance. Two flame structures are defined to consider different evaporation and flame histories of the two split injection fuel groups. An independent transport equation is solved for each fuel vapor group with no mutual interaction between flame structures. The local mean mixture fraction and its variance determine the probability density functions (PDF) and the scalar dissipation rates (SDR). Calculated pressure traces show reasonable agreement with measurements for different loads and ratios between the two split injections. The overpredicted rate of pressure rise at ignition is attributed to simultaneous burning of all combustible premixture in the CMC model. The flammable limits are applied to consider extinction of lean mixture, wall film, or other possible factors for incomplete combustion of the pilot injection fuel, which burns completely after mixing with the second main injection fuel. Further research may be required for improved spray atomization and wall film models, which play a significant role in heat release and emissions of pHCCI engines.