Thermoplastic elastomers are widely used in the medical industry for advanced medical and healthcare products, helping millions of patients achieve a better quality of life. Yet, microbial contamination and material-associated biofilms on devices remain a critical challenge because it is challenging for currently available materials to provide critical antifouling properties, thermoplasticity, and elastic properties simultaneously. We developed a highly flexible zwitterionic thermoplastic polyurethane with critical antifouling properties. A series of poly((diethanolamine ethyl acetate)-co-poly(tetrahydrofuran)-co-(1,6-diisocyanatohexane)) (PCB-PTHFUs) were synthesized. The PCB-PTHFUs exhibit a breaking strain of more than 400%, a high resistance to fibroblast cells for 24 h, and the excellent ability to prevent biofilm formation for up to three weeks. This study lays a foundation for clarifying the structure-function relationships of zwitterionic polymers. This thermoplastic PCB-PTHFU platform, with its unmatched antifouling properties and high elasticity, has potential for implanted medical devices and a broad spectrum of applications that suffer from biofouling, such as material-associated infection.