Computer methods with simplified mathematical models in conjunction with empirical model parameters can be efficiently practiced into an optimization of a diesel aftertreatment system. Components of prime interests are diesel particulate filter, diesel oxidation catalyst and de-$NO_x$ catalytic converter. de-$NO_x$, de-PM, and de-HC processes in each part are individually modeled, formulated and then combined into an integrated analysis procedure for a unified simulation of the diesel emission aftertreatment. The model is empirically tuned and validated with comprehensive engine and laboratory data. The effects of emission species and space velocity on the $NO_x$ and soot reductions are parametrically investigated. A lowered $NO_2/NO_x$ ratio due to PM oxidation in DPF contributes to promote the $NO_x$ reduction by SCR at intermediate gas temperatures. $NO_x$ reduction is inert to the PM oxidation at high temperatures. Rate of PM trapping strongly depends on temperature and $NO_x$ concentration.