Anionic emulsifiers, synthesized from novel silicone RAFT reagents (RAFT-PDMS), acrylic acid, lauryl methacrylate, and methyl methacrylate, were used to create a macromolecular silicone-modified polyacrylate aqueous emulsion. This emulsion was prepared by copolymerizing the custom-made anionic emulsifier with hydroxyethyl acrylate and other monomers. The emulsion underwent crosslinking with isocyanate, leading to a novel aqueous wood varnish incorporating polydimethylsiloxane chain segments. The structural features of RAFT-PDMS were characterized using 1HNMR, Fourier Transform Infrared Spectroscopy (FTIR), Ultraviolet-Visible Absorption Spectroscopy (UV–VIS), and Energy-Dispersive X-ray Spectroscopy (EDS). By adjusting the degree of polymerization and content of RAFT-PDMS, emulsions with a core-shell structure were generated. The impact of RAFT-PDMS on the molecular weight, particle size, and thermal properties of the latex was evaluated. Studies demonstrated that the applied wood coatings reduced surface roughness while enhancing gloss and hydrophobicity. Further tests revealed excellent antifouling properties and resistance to both acid and alkali for the coating. This type of wood paint could address challenges associated with the difficulty of combining large molecule organosilicones with wood, thereby offering a novel approach for wood paint applications.