The acrylic emulsion used for primer coating in BOPET film printing faces issues such as insufficient coating adhesion and poor compatibility with water/solvent-based inks, and semi-continuous seeded emulsion polymerization was employed. Using butyl acrylate (BA) and methyl methacrylate (MMA) as base monomers, functional modifying monomers such as isobornyl acrylate (IBOA), tetrahydrofurfuryl acrylate (THFA), and ureido acrylate (WAM-3), as well as crosslinkable monomers like trimethylolpropane trimethacrylate (TMPTMA) and diacetone acrylamide (DAAM), a core-shell acrylate emulsion with differentiated crosslinking density and surface activity was constructed. The effects of the shell layer’s glass transition temperature (Tg), core-shell mass ratio, and functional monomer content in the shell layer on the interfacial adhesion of BOPET films were investigated. The distribution of functional and crosslinkable monomers in the core and shell layers and their impacts on the adhesion compatibility of water-based and solvent-based inks on the coating were also studied. After optimizing the system parameters, the best interfacial bonding performance was achieved when the core Tg was -15 ℃, the shell Tg was 25 ℃, and the core-shell mass ratio was 3:7, and the adhesion performance was grade 0. When the shell layer contained 9.8% IBOA, 0.6% THFA, 0.8% WAM-3, and 2.4% TMPTMA, with post-crosslinking monomer DAAM at 2% in the core and 5% in the shell, the prepared core-shell structure acrylate emulsion demonstrated the best printing adhesion, rated as grade 0, for both water-based and solvent-based inks on BOPET film primers.