The formation of biofilm and thrombus on medical catheters poses a significant life‐threatening concern. Hydrophilic anti‐biofouling coatings upon catheter surfaces with complex shapes and narrow lumens are demonstrated to have the potential in reducing complications. However, their effectiveness is constrained by poor mechanical stability and weak substrate adhesion. Herein, a novel zwitterionic polyurethane (SUPU) with strong mechanical stability and long‐term anti‐biofouling is developed by controlling the ratio of sulfobetaine‐diol and ureido‐pyrimidinone. Once immersed in water, as‐synthesized zwitterionic coating (SUPU3 SE) would undergo a water‐driven segment reorientation to obtain much higher durability than its direct drying one, even under various extreme treatments, including acidic solution, abrasion, ultrasonication, flushing, and shearing, in PBS at 37 °C for 14 days. Moreover, SUPU3 SE coating could achieve a 97.1% of exceptional reducing protein fouling, complete prevention of cell adhesion, and long‐lasting anti‐biofilm performance even after 30 days. Finally, the good anti‐thrombogenic formations of SUPU3 SE coating with bacterial treatment are validated in blood circulation through an ex vivo rabbit arteriovenous shunt model. This work provides a facile approach to fabricating stable hydrophilic coating through a simple solvent exchange to reduce thrombosis and infection of biomedical catheters.