It has been widely known that thermal and fuel stratifications of in-cylinder mixture are effective to reduce in-cylinder pressure rise rate during high load HCCI operations. In order to optimize a combustion chamber design and combustion control strategy for HCCI engines with wide operational range, it is important to know quantitatively the influence of the temperature and fuel concentration distributions on ignition and heat release characteristics. At the same time, it is important to know the influence of in-cylinder flow and turbulence on the temperature and fuel concentration distributions. In this study, a numerical simulation of HCCI combustion were conducted to investigate the effects of the in-cylinder flow and turbulence, and the distributions of temperature on ignition and combustion characteristics in HCCI combustion. As a result, the initial temperature distribution of the cylinder air-fuel mixture was found to be effective for slowing the combustion because the large distribution of the scale is not easily influenced by the mixing due to the flow. In addition, it was found that the combustion slows down when the temperature gradient is wide in the combustion region.