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We have developed a model-based control for the air intake system in a variable valve engine, employing total engine simulation, the response surface method and multi-objective optimization scheme. In our technique, we performed the simulation model tuning and validation, followed by the creation of a dataset for the polynomial regression analysis of the charging efficiency. A D-optimal design, robust least squares method, and likelihood-ratio test were demonstrated to yield a robust and accurate control model. Coupling the total engine simulator with a genetic algorithm, model based calibration for optimal valve timing stored in lookup table was carried out under multiple objectives and restrictions. The reliability of the implementation control model, which considers the effect of gas dynamics in the intake system, was confirmed using a model-in-the-loop simulation.