Problem of HCCI combustion is knocking due to a steep heat release by the ignition that is occurred in each local area at the same time. It is considered that dispersion of auto-ignition timing at each local area in the combustion chamber is necessary to prevent this problem. One of technique of this solution is to make thermal stratification. It could be made by using two-stage ignition fuel, which has large heat release at low temperature reaction. Dispersion of fuel concentration leads to difference of temperature histories while combustion phasing is dispersed at each local area. Also, EGR gas stratification could make difference of temperature histories at each local area because of that of the characteristics. This study examines the effect of mixing stratification by stratifying the charge of fuel and CO2. A single-cylinder engine equipped with optical access was used in experiments, and numerical analysis was executed. This study shows that stratified mixtures of the fuel and EGR gas make differences of the temperature histories at each local area, which results in difference of the combustion phasing at each local area in combustion chamber and reduction of PRR.