Self-migration or unstable phase inversion occurs when the application conditions are varied, which limits the application of polyurethane-acrylate (PUA) composite films. In this paper, cross-linked polyurethane/poly(methyl methacrylate-co-borneol acrylate) shell microspheres were prepared by using the seeded emulsion polymerization method. The core-shell structure of these samples was identified by dynamic light scattering (DLS) and high-resolution transmission electron microscope (HR-TEM). Moreover, HR-TEM images indicated that the core-shell structure of the microsphere does not undergo complete phase inversion. In addition, with increasing content of borneol acrylate in the shell, the water resistance and antibacterial adhesion of films were improved. The X-ray photoelectron spectroscopy (XPS), Energy Dispersive Spectrometer (EDS), water contact angle (CA) measurements, antibacterial and anti-adhesion tests demonstrate that the C/N ratios of films from the inside to the upper surface had an obvious gradient in growth, indicating the shell component (polyborneol acrylate) was predominantly present at the surface of films after coalescence in cross-linked core-shell PUA. It was found that a suitable degree of cross-linking contributes to the segregation of the hydrophobic component (borneol groups) on the film surface. As a consequence, the excellent water resistance, cytocompatibility, and antibacterial properties endowed this series of polymer materials with promising application potential in the biomedical field.