An on-the-fly mechanism reduction approach is employed in this paper to integrate detailed chemical kinetics with a computational fluid dynamics (CFD) code. The reduction methodology employs an instantaneous element flux analysis to identify redundant species and reactions for given local conditions. The emphasis of this work is focused on the numerical study of homogeneous charge compression ignition (HCCI) engine combustion in CFD code KIVA-3V using a detailed n-heptane oxidation mechanism with 633 species and 2827 elementary reactions. The proposed on-the-fly reduction method predicts species concentrations, temperatures, and pressures with high fidelity compared to solutions obtained using the detailed mechanism. In the mean time, central processing unit (CPU) time on chemistry calculation is tremendously reduced, enabling integration of complex kinetic mechanisms in engine CFD. When detailed chemistry is combined with realistic flow simulation, accurate predictions of in-cylinder combustion behavior of HCCI engines are provided.