Isocyanate‐based monomers and polymers have found widespread industrial application; however, the realization of green water‐based products via the preparation of stable isocyanate aqueous emulsions remains challenging. Herein, a series of organosilicon and organofluorine synergistically modified amphiphilic branched polyurethanes (HBWPU), synthesized by grafting perfluorohexyl ethanol semi‐terminated isophorone diisocyanate (IPDI) onto a hydrophilic polyurethane prepolymer, is presented. Subsequently, using a physical mixing method, stable diisocyanate emulsions are fabricated by preparing diisocyanate latex particles with IPDI as the core and hyperbranched water‐based polyurethanes (HBWPU) as the shell. Structural investigations showed that the branching degree and fluorine content of the HBWPU significantly affects the stability of the diisocyanate emulsions. Increasing the degree of branching from 0.34 to 0.86 causes the amount of residual isocyanate (NCO) groups to decrease from 20.1% to 16.7%. In contrast, an increase in the fluorine content from 0% to 17.8% increases the amount of residual NCO groups from 11.5% to 24.6%. Thus, HBWPU can be used as an emulsifier to prepare waterborne diisocyanate cross‐linking agents. Such polyurethane‐coated isocyanate aqueous emulsions can increase the hardness and significantly improve the acetone resistance of hydroxyl polyacrylate resins.