Water-based materials are important to mitigate the concern on solvent-based products. Incorporation of reactive isocyanate-based crosslinking agents is key to improve material performance, while intense, nonhomogeneous reaction causes short operation duration and uncontrollable product quality. Herein, this study proposes a Hw-Ho-NCO (hydrophilic part-hydrophobic segment-NCO group) structural model to overcome such issue by forming water-compatible isocyanate emulsions via self-emulsification of castor oil-modified water-dispersible isocyanate (WDI). The properties of WDI and obtained emulsions were analyzed through visual appearance, titration of -NCO content, droplet size determination, microstructure, etc. Aggregation and sedimentation of the isocyanate emulsions upon storage occur owing to lack of hydrophilic groups on droplet surface, while sodium dodecyl sulfate (SDS)-assisted secondary emulsification improves the emulsion stability. The emulsions are used as crosslinking agents to formulate composite waterborne adhesives with the white latex (EVA-102), reaching maximal pot life of 8 h. The plywood specimens manufactured using the composite adhesive show enhanced adhesion performances, particularly for wet strength I and II, exceeding the Chinese national standard (GB/T 9846–2015). This study confirms the capability of using the structural model to create stable isocyanate emulsions that can target to formulate high-performance waterborne adhesives for clean and green production in wood industry.