Nowadays, computer models have contributed to a better understanding and solution of long standing practical combustion problems in HCCI (homogenous charge compression ignition) engines. In this study, a new multi zone model is developed for HCCI engines simulation. Model contains four different types of zones, which are core, boundary layer, zones between them, and crevice zone. Heat and mass transfer are considered between all of zones. For accurate calculation of initial conditions at IVC, multi zone model is coupled with a single zone model, which simulates gas exchange process. The developed model is validated by using two types of fuels, n-heptane as a fuel with low octane number and methane as a fuel with high octane number. Semi detailed chemical kinetics mechanisms of fuels are used for their combustion simulation. A new heat transfer model is used for calculating convective heat transfer, which enhanced the model ability in prediction of combustion and performance characteristics of engine accurately. Model results are in good agreement with experimental data in prediction of in-cylinder pressure, NOx, CO and UHC emissions. Accurate mass transfer model caused to accurate prediction of UHC (maximum error is 20.2%) and CO (maximum error is 1.8%). Near zero NOx, which is lower than 10 ppm for all of examined cases, is predicted well, too. (C) 2014 Elsevier Ltd. All rights reserved.