The increasing global focus on sustainability and environmental protection has driven significant developments in research on waterborne pressure-sensitive adhesives (PSAs). Among these, hexafluorobutyl methacrylate (HFMA)-modified core-shell polyacrylates show great potential as waterborne PSAs but are hindered by limited understanding of HFMA's effect on PSA properties. To address this challenge, we successfully synthesized a series of core-shell polyacrylate latex PSAs using (meth)acrylates as the primary monomer and HFMA as the modifying monomer, employing a monomer-starved seeded semi-continuous emulsion polymerization process. Comprehensive characterizations, including FTIR, XPS, DSC and TEM, confirmed the successful incorporation of HFMA into the latex copolymer and the formation of core-shell structures. Notably, increasing the HFMA content from 0 to 20 wt% significantly reduced the water absorption rate of the latex films from 15 to 4 wt% and decreased the surface tension from 42 to 34 mN/m. Concurrently, the water contact angle and water whitening resistance were greatly enhanced. Additionally, the loop tack and peel strength of the modified PSAs were improved by 81 and 89%, respectively. Furthermore, all PSA samples demonstrated high shear strength (> 72 h) and gel content (> 69 wt%), achieving a remarkable balance between cohesion and adhesion. This work offered a novel approach for designing waterborne PSAs with excellent water whitening resistance and high cohesion, broadening the possibilities for sustainable adhesive applications.