The optimal design of high wear‐resistance and durability of coatings using organic–inorganic interpenetrating networks has been a long‐term goal of researchers. Although some progress has been made in the modification of waterborne polyurethanes (WPU), there are still significant challenges in fabricating more durable polyurethane‐based protective coatings from the perspective of structural design at a molecular level. Here, a sub‐nanoscaled (<1 nm) inorganic calcium phosphate oligomer (CPO) is used to carry out organic–inorganic hybrid cross‐linking in a WPU network and precisely regulate the structure of the macromolecular network at the molecular level. The herein‐produced CPO‐WPU hybrid coating shows excellent wear resistance and water resistance. Taber abrasion tests demonstrate that the CPO‐WPU coating can be capable of 15 500 turns at a load of 750 g, 2.2 times that of pure WPU coating, and the water‐resistance of CPO‐WPU coating is significantly improved compared with WPU coating due to its well‐integrated organic–inorganic network. Overall, the CPO‐WPU coating material significantly improves the mechanical strength, wear‐resistance, and water‐resistance, compared with the original WPU coating and other modified polyurethane. This hybrid coating can provide a potential application in paper‐making, textiles, and furniture due to its unique organic–inorganic network, low cost, and green process.