Vibration of intake menifold is important as it could worsen the noise levels radiated from surface itself and support bracket, and it eventually leads to the failures of a Throttle Position Sensor and an Idle Air Control Valve. In this study, structural modification method is proposed to reduce structural vibration of an intake manifold system. At first, vibration problems are identified through tests on a running engine. Then modal data acquired by modal testing and finite element analysis are helpful to understand vibration mechanism of the system, and used as the design guide when structural modifications are attempted. After the system model is validated by comparison of the modal data obtained from analysis and experiment, iterative calculations are performed to find optimized structure of the system by finite element analysis. As a result, a newly designed plenum bracket is suggested in such a way that the intake manifold is stiffened, and that design of the support bracket is suggested in such a way that the intake manifold is stiffened, and that design of the support bracket is changed in terms of bolting position, thickness, shape, and minimum weight increase. Finally, it is shown that a new design achieves a significant reduction of vibration of an intake manifold system and it is confirmed by tests on a running engine.