The invention discloses a hydrophobic membrane based on fluorine-containing polyurethane and a preparation method of the hydrophobic membrane. The preparation method comprises the following steps: spin-coating the fluorine-containing polyurethane into a film; curing to obtain the hydrophobic membrane based on the fluorine-containing polyurethane; taking fluorine-containing alkyl polyether glycol and diisocyanate to be subjected to addition polymerization reaction; and catalyzing through a tin catalyst and extending a chain through a chain extender; and adding an amino silane coupling agent and capping an end to prepare the fluorine-containing polyurethane. The product has a fluorine-containing polyether block and high fluorine content; perfluoroalkyl located at a polyether side easily has micro-phase separation and surface migration; the surface energy of the polyurethane is low; and the fluorine-containing polyurethane is subjected to end capping by the silane coupling agent and is easy to store and easy to cure. The hydrophobic membrane based on the fluorine-containing polyurethane, disclosed by the invention, has a water contact angle higher than 110 degrees and good water repellency.