Very small amount of NOx and soot emissions and also higher thermal efficiency in comparison with conventional engines are the well known benefits of the homogeneous charge compression ignition (HCCI). Because of the absent of any external source, the auto ignition of well-mixed in-cylinder charge is responsible for combustion. The thermal conditions of the combustion chamber are governed by the interaction of the chemical processes with the temperature and pressure histories which is affected by heat transfer from the hot gas to the walls. As a result, the heat release rate and heat transfer inside the combustion chamber play a significant role in the HCCI combustion mode. However, in developing reduced chemical kinetic mechanism from the detailed chemical kinetic mechanism it is common to not consider heat transfer to focus on the kinetics aspects of HCCI. The objective of this work is to investigate the effects of heat transfer through the boundaries in HCCI combustion simulation in generating reduced mechanism from the detailed mechanism. A single-zone combustion model is used to simulate the HCCI engine. A two-stage reduction process is used to produce reduced mechanisms of existing semi-detailed GRI-Mech. 3.0 mechanism. To remove unimportant species, at the first stage, the directed relation graph with error propagation (DRGEP) is applied. In the second stage, the principal component analysis (PCA) method is used to eliminate insignificant reactions. Several different operating conditions are considered. Matching pressure, temperature and cumulated heat release traces and also the mass fraction of some important species calculated from both of the reduced mechanisms agree closely with the results obtained from detailed mechanism. Small differences observed in the developed reduced mechanisms for HCCI combustion model with considering heat transfer and in the adiabatic condition.