To investigate the damping characteristics of poly(ether ether ketone) (PEEK), various potential modifications of the molecular structure, including sulfonate groups, hydroxyl groups, amino groups, carboxyl groups, methyl groups, fluorines, and benzene rings, were considered. It was found that these functional groups can mediate both the storage and loss modulus of PEEK derivatives, and the loss factors of PEEK derivatives are sensitive to the content and type of functional groups, indicating an ideal designability of energy dissipation performance. The reciprocating process of H-bonds and C π −H bonds breaking and reforming during material deformation and the available free volume in the material are critical to the energy dissipation capacities in polymers.