An optimal design method of vibration isolation system suitable for complex structures under stationary random excitation is proposed. This new method determines the installation position of vibration isolators and optimum control force on the determined positions,and searches for the optimal parameters of the vibration isolators on the basis of optimized control forces. Therefore, the forces translated by the isolators to the main systems can be made very much closer to the optimized control force and vibration level is lower than the permitted level. The repeated analyses of the system dynamic characteristics can be omitted a lot and the calculation speed can be quicken very much, the optimal installation positions and parameters can be obtained simultaneously. Because the prerequisite that the modes do not affect each other is not used, it can certainly be applied to the complex structures conveniently.