Homogeneous charge compression ignition (HCCI) is a promised solution to environmental and fuel economy concerns for IC engines. Engine application for HCCI engine depends on an array of parameters such as fuel type, mixture composition, intake condition and engine specification, meaning that controlling an HCCI engine can only be done through the adjustment of these parameters. In this numerical study which is driven from an experimental work, thermal and charge stratification is used to control HCCI combustion. The effect of intake temperature, compression ratio, intake pressure, EGR, reformer gas (CO-H2 mixture) and glow plug temperature on engine performance and emission was investigated using a 3D model on AVL-FIRE parallel with 1D model on GT-Power software. Then AHP model as a multiple Attribute Decision making method has been used to analyze the sensitivity of these parameters on performance and emission. Results indicate that increasing intake temperature causes the operating condition approaches knock which results in a narrower operating region. Increasing EGR ratio makes possible the expanding of operating range rich limit since it causes delayed combustion start, prolonged combustion duration and avoids knocking. The use of reformer gas expands the operating range lean limit and increases the possibility of engine well operation in this region. However, the change in reformer gas composition does not have a great influence on combustion. Using glow plug advances combustion while prolonging burn duration. Therefore, in-cylinder thermal stratification pushes engine operating points toward rich limit and as a result high power achievement becomes possible. Finally the sensitivity analysis results show that in the studied range the EGR is the most effective parameter on combustion. In this analysis, the sensitivity of inlet pressure, reformer gas ratio, compression ratio, inlet temperature, reformer gas composition, and glow plug temperature point are in the next ranks respectively.