Waterborne polyurethane (WPU) often suffers from poor water resistance and mechanical properties due to hydrophilic emulsifiers. To address these issues, this study introduces glycidyl carbamate (GC) as a crosslinker to improve WPU performance. Three types of GC were synthesized using aliphatic, cycloaliphatic, and aromatic isocyanates, respectively. The crosslinked network was established through a reaction between the epoxide group of GC and the carboxylic acid and amine groups of WPU. Among these, the WPU film utilizing aromatic isocyanate-based GC exhibited the highest crosslink density, modulus, hardness, and water resistance, due to the rigidity of the aromatic molecular structure. However, the film displayed excessive brittleness, resulting in reduced tensile strength, along with yellowing typically associated with aromatic compounds. The WPU crosslinked with cycloaliphatic GC demonstrated the next best mechanical properties and water resistance, with a 2.7-fold increase in tensile strength, a 1.5-fold increase in hardness, and a 66% reduction in the water swelling ratio compared to neat WPU. This study presents a novel and effective strategy to enhance the water resistance and mechanical properties of WPU films, making them suitable for advanced coating applications.