The invention belongs to the technical field of preparation of waterborne polyurethane, and discloses a preparation method of fluorine-containing soybean-oil-based waterborne polyurethane. The preparation method specifically includes the steps that epoxidized soybean oil is subjected to a ring-opening reaction through trifluoroacetic acid to obtain fluorine-containing soybean-oil-based polyhydric alcohol, then fluorine-containing soybean-oil-based polyhydric alcohol is reacted with diisocyanate and hydrophilic monomers to generate fluorine-containing soybean-oil-based polyurethane prepolymers, triethylamine is added to be neutralized with carboxyl, deionized water is added for emulsification, then ethylenediamine is added for chain extension, and fluorine-containing soybean-oil-based waterborne polyurethane is obtained. According to the preparation method, an existing technology is improved, namely, soybean oil polyhydric alcohol which is a renewable resource is used for replacing a petroleum product, and the preparation method of fluorine-containing soybean-oil-based waterborne polyurethane is environmentally friendly.