Advancing the development of eco‐friendly waterborne polyurethane elastomers (WPUEs) can significantly reduce the reliance on organic solvents, which is crucial for environmental conservation. Nevertheless, achieving superior mechanical properties and self‐healing capabilities in WPUEs presents a considerable challenge. Drawing inspiration from the hierarchical dynamic structures observed in scallop byssal threads, a high‐strength supramolecular waterborne polyurethane elastomer (SWPUE), designated SWPU‐DESH‐Zn, is developed in this study. Owing to the precise regulation of the hydrogen bonding state of acylsemicarbazide (ASC) fragments via disulfide bonds, and the formation of coordination interactions between carboxyl and zinc ions, the as‐prepared elastomer exhibited a robust mechanical strength of 52.07 MPa, comparable to that of solvent‐based polyurethane elastomers. Additionally, it exhibited notable self‐healing capability and excellent reprocessability. Meanwhile, high‐performance ionic skins and electromagnetic interference (EMI) shielding materials are also fabricated using SWPU‐DESH‐Zn as the matrix, further illustrating its potential applications. This novel biomimetic approach, inspired by scallop byssal threads, offers valuable insights for designing healable waterborne polymers with enhanced mechanical properties.