In this study, a phenomenological combustion model, which had been developed based on a stochastic combustion model for simulating combustion with multi-stage injection in diesel engines, was improved to estimate the NOx and soot emissions with modifications in the model for the interaction of sprays from sequent injection stages. Model validation was performed by comparison with experimental data from a single-cylinder diesel engine. To understand the variation of NOx and soot production with injection conditions, analysis of combustion process was conducted based on the calculation results from different injection parameters including injection timing and quantity.