Both concentration stratification and reactivity stratification are beneficial for reducing the combustion rate and controlling the combustion phasing in HCCI (homogeneous charge compression ignition) operation. However, the different effects on combustion and emissions of concentration and reactivity stratification have not been fully explored and the interaction between the two stratification modes also needs to be clarified. Therefore, the effects of concentration stratification and reactivity stratification on combustion and emission characteristics were investigated in a single-cylinder diesel engine. The different concentration stratifications were designed by five port injection ratios to study the influence of concentration stratification. Cases with and without reactivity stratification were compared at the same overall reactivity and the same concentration stratification in the cylinder to roughly separate the impact of reactivity stratification. Results show that with the decrease of the premixed ratio, the peak heat release rate decreases, combustion phasing delays, and the thermal efficiency show the tendency of first decreasing and then increasing. For cases with same concentration stratification, the introduction of iso-octane/n-heptane reactivity stratification decreases combustion efficiency but increases indicated thermal efficiency, NOx (nitrogen oxides) emissions can be improved while CO (carbon monoxide) and HC (hydrocarbon) emissions are increased. The introduction of n-heptane/iso-octane reactivity stratification presents a positive effect on both thermal efficiency and combustion efficiency and contributes to the improvement in NOx, CO and HC emissions.