The free vibration behaviors of the embedded and co-cured perforated damping sandwich composite (ECPDSC) in which the holes are filled with resin are investigated. The displacement field of laminated structure and the equivalent elastic parameters of the heterogeneous damping layer are presented by the combination of the first order shear deformation theory with homogenization method. The dynamic equations of the structure are derived on basis of the equivalent complex modulus theory, and the theoretical results are verified by experimental platform. The relationships of damping area ratio and the thickness of damping layer as well as the elastic modulus of viscoelastic material with the dynamic properties of ECPDSC are theoretically explored further. Results indicate that the modal frequency decreases slowly when the damping area ratio is relatively small, the modal frequency decreases rapidly when the damping area ratio is relatively large, and the trend of loss factor is just opposite. This investigation will lay a foundation for the design and manufacture of composite components with light weight, large damping as well as high stiffness.