In this work, a series of polymer microcapsules based on UV-curable prepolymers are prepared by combining an emulsion template and photopolymerization. The modulation of the shell structure is achieved by employing UV-curable prepolymers with different chemical structures (polyurethane acrylates, polyester acrylates, and epoxy acrylates) and functionalities (di-, tetra-, and hex-). The relationships between the shell structure and the microcapsule properties are investigated in detail. The results show that the properties of the microcapsules can be effectively regulated by adjusting the composition and cross-linking density of the shell. Epoxy acrylate-based microcapsules exhibit higher impermeability, solvent resistance, and barrier and mechanical properties than polyurethane acrylate and polyester acrylatebased microcapsules. Using UV-curable prepolymer with high functionality as a shell-forming material could effectively improve the impermeability, solvent resistance, and barrier and mechanical properties of microcapsules. In addition, the dispersion of microcapsules in the coating matrix tends to follow the "similar component, better compatibility" principle, i.e., a uniform dispersion of the microcapsule in the coating matrix is more easily achieved when the compositions of the microcapsule shell and coating are similar in structure. The convenient adjustment of the shell structure and the investigation of the "structure−property" relationship provide guidance for the further controlled design of microcapsules.