In this study, the effects of Variable Valve Timing (VVT) on the performance of a Homogeneous Charge Compression Ignition (HCCI) engine are analyzed by developing a computationally efficient modeling approach for the HCCI engine cycle. A full engine cycle model called Sequential Model for Residual affected HCCI (SMRH) is developed using a multi zone thermo-kinetic combustion model coupled with flow dynamic models. The SMRH utilizes CHEMKIN®-PRO and GT-POWER® software along with an in-house exhaust gas flow model. Experimental data from a single cylinder HCCI engine is used to validate the model for different operating conditions. Validation results show a good agreement with experimental data for predicting combustion phasing, Indicated Mean Effective Pressure (IMEP), thermal efficiency as well as CO emission. The experimentally validated SMRH is then used to investigate the effects of intake and exhaust valve timing on residual affected HCCI engine combustion. A new Fuel Efficiency and Emission (FEE) index is defined to optimize engine performance. SMRH is used as a virtual engine test bed to generate FEE contour maps as a function of valve timings. The simulation results determine optimum valve timings with the highest FEE index. The results indicate the SMRH is of utility for design of VVT strategies to control the HCCI engine in optimum regions with low engine-out emissions and low fuel consumption.