The invention provides a preparation method of organic fluorine modified hyperbranched water-based polyurethane. The method comprises the following steps: (1), synthesizing water-based terminal hydroxyl hyperbranched polyurethane core; (2), synthesizing a double bond end capped linear polyurethane prepolymer through diisocyanate, low polymer divalent alcohol, a chain extendor, an end-capping reagent and the like; (3), grafting linear polyurethane onto terminal hydroxyl hyperbranched polyurethane; (4), leading a fluorine element onto a polymer through an emulsion method, so as to obtain the organic fluorine modified hyperbranched water-based polyurethane. According to the organic fluorine modified hyperbranched water-based polyurethane provided by the invention, raw materials are cheap and readily available, and are wide in sources, the synthesis process is simple, and industrialized production is facilitated. The organic fluorine modified hyperbranched water-based polyurethane is appropriate to be used independently, can be matched with other water-based resins, can be applied to the fields of water-resistant paints, environment-friendly water-based adhesives, water-based paints and the like, and has a broad application prospect.