The invention discloses a preparation method of fluorine-containing cation acrylate resin cathode electrophoresis paint. The preparation method includes: preparing cation fluorine-modified acrylate resin and a totally enclosed polyisocyanate crosslinking agent, and acidizing the same after reaction; sufficiently mixing with hydrophobic oxide particles; adding deionized water, and dispersing to obtain the cathode electrophoresis paint. Fluorine-modified acrylate monomer is introduced in the acrylate resin cathode electrophoresis pain, and excellent chemical resistance and low surface energy of fluorine-containing resin are utilized, so that hydrophobicity of a paint film is improved effectively; the hydrophobic alumina particles have excellent hydrophobicity. By adding this novel modifier, hydrophobicity of the paint is improved greatly, and the key difficulty that the electrophoresis paint is difficult to stably store and utilize caused by the fact that an electrophoresis emulsion is difficult to disperse due to existence of the fluorine-containing resin in the paint is improved.