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In recent years, entirely combined CFD-Multi-Zone chemistry combustion models have been developed fashionably in investigating the HCCI engine combustion. In this work, an enhanced Multi-zone chemistry model is recommended for the HCCI engine combustion and emission simulation. There are four sorts of zones enclosing the crevice zone; boundary layer zone, external zones and center zone of the engine cylinder have been applied. The volume of each zone is steady and depends on the engine geometry. The boundary layer zone is the closest zone to the engine cylinder wall. In this study, the reduced chemical kinetic oxidation mechanism of diesel/biodiesel-ethanol has been numerically investigated in homogenous charge compression ignition (HCCI) engine. The oxidation mechanism of the diesel oil-biodiesel-ethanol at different blends was developed and coupled with Multi-Zone chemical kinetics model.