The invention relates to a preparation method of a high-hydrophobicity leather coating agent. The acrylate leather coating agent has excellent film-forming property, light stability, weather resistance and binding property, but has some defects, such as poor water resistance, poor solvent resistance, lack of functionality and the like, due to the linear structure of the acrylate resin. In order to overcome the defects above, the invention provides a semicontinuous seed emulsion polymerization method for preparing the core-shell acrylate resin: the shell is properly cross-linked, so that the acrylate resin is converted into a reticular structure from the linear structure, thereby enhancing the water resistance and solvent resistance of the acrylate resin; and besides, organic fluorine is introduced into the shell, so that the acrylate resin has high hydrophobicity. After the high-hydrophobicity leather coating agent forms a film, the contact angle with water is up to 124 degrees, and the film feels smooth and not sticky; the 24-hour water absorptivity is less than 10%; and after being soaked in methylbenzene for 48 hours, the film only swells, but is not dissolved.