EGR (Exhaust gas recirculation) stratification is a promising solution proposed to control incylinder distribution to decrease NOx and PM (Particular matter) generation during combustion process. The key issue of EGR stratification is to control incylinder distribution. A novel method called timing sequential intake strategy which divides the intake process into several periods and controls different intake charge flows into engine cylinder for each period was proposed and investigated by computation fluid dynamics (CFD) technology. The simulation model was established based on a heavy duty diesel engine. It is indicated that intake charge in earlier intake period was rich at the bottom of combustion chamber while the later charge was rich at the upper center of combustion chamber near compression top dead center. It is feasible to obtain axial stratification using timing sequential intake strategy. The combustion pressure and temperature were lower than those of uniform intake strategy which supplying the mixture of intake CO2 and fresh air during the whole intake process. Compared to the uniform intake strategy, the start of combustion delayed about 0.7°CA, however, the peak value of heat release rate was much higher, NOx emissions were decreased by 51.2%, and PM emission was decreased by 13.4%. Timing sequential intake strategy needs to be further investigated as it is beneficial for both reductions of NOx and PM emissions and fuel consumption.