The invention relates to the field ship antifouling coatings, in particular to a nanometer polysiloxane nontoxic low-surface-energy ship antifouling coating for sea ships and a preparation method thereof, which are used for solving the problem of long-term nontoxicity, antifouling and corrosion on the outer bottom surface of a ship. The nanometer polysiloxane nontoxic low-surface-energy ship antifouling coating comprises the following components in parts by weight: 50-55 parts of polysiloxane resin, 1-5 parts of nanometer slurry, 5-8 parts of dimethylbenzene, 6-10 parts of butyl ester; 2.0-3.0 parts of ethylene glycol diethyl ether acetic ester, 0.3-0.5 part of a dispersing agent, 0.3-0.5 part of an antifoaming agent, 0.1-0.3 part of a flatting agent, 0.5-0.8 part of an anti-settling agent, 0.4-0.7 part of gas phase white carbon black, 15-22 parts of a pigment and 3-6 parts of a filler. The preparation method comprises the following steps of: proportionally preparing, dispersing, and grinding till the fineness is below 30 micros to obtain a component A; and mixing the component A and the component B for curing to obtain the nontoxic long-term ship sea antifouling coating. The nanometer polysiloxane nontoxic low-surface-energy ship antifouling coating is a surface protection material with extreme low surface energy, and plays roles in preventing fouling and scaling, and marine organisms are prevented from being adhered to the antifouling coating easily.