Damping capacity and stiffness loss must be considered together in the design of integral damping composite structures. In the present paper, a discrete layer beam finite element is used to model and analyze a damped composite I-beam embedded with viscoelastic layers. Two multi-objective optimization models are developed with maximum natural frequency and modal loss factor. In the first model, only one damping layer is embedded in each flange of the I-beam. Design variables consist of damping layer thickness and its inserting location. In the second model, multiple damping layers of equal thickness are embedded in the flanges. Design variables included the number of damping layers and their inserting locations. Multi-objective genetic algorithm is used to solve optimization problems. It is showed that the analysis method has acceptable accuracy for composite damped I-beams, and it is convenient for optimization design of integral damping composite structures, especially for the cases embedded with multiple damping layers.