A nine-zone model accounting for both mass exchange and heat loss was developed by modifying the SENKIN program. Combining with the SKLE simplified chemical kinetics model of n-heptane, the model was used to simulate the combustion and emissions of homogeneous charge compression ignition (HCCI) engine with charge-temperature stratification. The results showed that the simulation is able to reproduce the major combustion and emission characteristics of the experiments very well. In HCCI engine with charge-temperature stratification, the outer core zone, the boundary zone and the crevice zone are the source of CO and HC emissions. The CO and HC emissions in the outer core zone result from the partial-oxidation and unburned fuels which flow into the outer core zone from both the boundary zone and the crevice zone at the expand stroke. Most of NOx emissions are produced in the inner core zones with higher temperature compared to the other zones. High efficiency combustion and extra low emissions are achieved simultaneously by increasing the wall temperature properly in HCCI engine with charge-temperature stratification.