The purpose of this study is to gain a better understanding of the effects of thermal stratification and partial fuel stratification on reducing the pressure-rise rate and emission in HCCI combustion. The engine is fueled with Di-Methyl Ether(DME) which has unique 2-stage heat release. Computational work is conducted with multi-zones model and detailed chemical reaction scheme. Calculation result shows that wider thermal stratification and partial fuel stratification prolong combustion duration and reduce pressure rise rate. But too wide partial fuel stratification increases CO and NOx concentration in exhaust gas, and decreases combustion efficiency.