Though hindered phenol/polymer-based hybrids show great potential in damping fields, the application of the materials is limited due to the irregular migration and self-aggregation of hindered phenol. To overcome this problem, 8-layered polyurethane (TPU)-polyvinyl acetate (PVAc) with varying phenol content in the polyurethane layer was fabricated using coextrusion. The distinct multilayer microstructure was first observed through the scanning electron microscopy. Subsequent molecular dynamics simulation revealed a directional migration of the hindered phenol to the interface without self-aggregation, existence of intermolecular hydrogen bonds between TPU (or PVAc) and hindered phenol, promoted diffusion of TPU and PVAc layers and reduced free volume. Then, the structure evolution was associated to the enhanced damping properties of the multilayer hybrids by the combination of the results of dynamic mechanical analysis.