The invention relates to graphene-fluorine modified waterborne polyurethane resin which is prepared through chemical reaction of polyisocyanate, polyhydric alcohol, a polyamine chain extender, oligomer polyhydric alcohol, dimethylolpropionic acid, graphene, hydroxy acrylic acid, fluoroalkene monomer, acrylic acid monomer, a neutralizing agent and deionized water. The invention also provides a preparation method of graphene-fluorine modified waterborne polyurethane resin. The prepared graphene-fluorine modified waterborne polyurethane resin has good properties of adhesion, stain resistance, high hardness, corrosion resistance, durability, hydrophobicity, static resistance, self cleaning and the like and can be applied to single-component waterborne coating, dual-component waterborne coating and normal-temperature curing coating and is widely applied to waterborne wood coating, waterborne industrial coating, waterborne antifouling coating, waterborne anticorrosion coating, waterborne antistatic coating and waterborne special engineering coating such as wind power generation, nuclear power and marine coating.