Traditional marine antifouling coatings function through releasing toxic antifouling agents, causing serious harm to marine ecosystems. To address this challenge, an eco-friendly fluoro-silicon-modified polythiourethane (FSi-PTU) coating has been prepared via a polymerization reaction with dihydroxy propyl silicone oil (HO-PDMS-OH), 1H,1H,2H,2H-perfluorohexanol (FTOH), hexamethylene diisocyanate (HDI), and pentaerythritol tetrakis (3-mercaptopropionate) (PETMP). The FSi-PTU polymer incorporates siloxane segments and fluorinated side chains, which are inhomogeneously distributed on the coating surface and construct a hydrophobic surface. The FSi-PTU coating exhibits good hydrophobicity, strong adhesion (≥2.14 MPa), and improved mechanical properties. The antifouling properties of the FSi-PTU coating have been researched. The results of laboratory tests demonstrate that the FSi-PTU coating exhibits excellent anti-protein adsorption and anti-algal attachment performance. The FSi-PTU-2 coating shows certain antifouling properties in the actual seawater test for three months. The results provide a certain reference value for developing eco-friendly marine antifouling coatings.