The importance of using biodiesel as an alternative in diesel engines has been demonstrated previously. A reduction in the soot, CO and HC emissions and an increase in the NO emission burning biodiesel fuels were reported consistently in previous technical papers. However, a widely accepted NO formation mechanism for biodiesel-fueled engines is currently lacking. As a result, in past multi-dimensional simulation studies, the NO emission of biodiesel combustion was predicted unsatisfactorily. In this study, the interaction between the soot and NO formations is considered during the prediction of the soot and NO emissions in a biodiesel-fueled engine. Meanwhile, a three-step soot model and an eight NO model which includes both the thermal NO mechanism and prompt mechanism are implemented. To simulate biodiesel combustion, a biodiesel combustion model containing 56 species and 158 reactions is currently developed based on an existing reduced model which consists of 53 species and 156 reactions. The results show that the predicted in-cylinder pressure using the current combustion model matches well with the experimental measurements. The ignition delay of the biodiesel combustion is also satisfactorily predicted using the current biodiesel combustion model. It is found that an increase in the soot formation leads to a reduction in the NO formation as the soot formation and the prompt NO formation compete for the CH species. The results also reveal that the NO emission is underpredicted using a NO model without the prompt NO mechanism. The NO emission in the biodiesel engine is acceptably predicted in this study. Moreover, the trend of the lift-off length changing versus crank angle is also reasonably predicted using the current biodiesel combustion model.