A linear polysiloxane copolymer (PSI) was synthesized via hydrolysis of three siloxane monomers followed by hydrolytic condensation. Then, butyl acrylate monomers were used for grafting and cross-linking PSI copolymer under photoinitiation. The resulting poly(butyl acrylate)-grafted polysiloxane (PBA-g-PSI) exhibited different morphologies and microphase separation structures by varying the weight ratio of PSI and PBA. Inspired by the gradient structure of biological materials, a novel gradient multilayer polymer was prepared by assembling different PBA-g-PSI layers. The unique microstructure of gradient multilayer polymer and microphase separation of PSI showed enhanced damping performance such as high tan delta(max) and low damping temperatures. In addition, the thermal stability and thermo-mechanical property with damping mechanisms of these gradient multilayer polymers were also studied.