We reported herein the synthesis of block copolymers and their application in the in-situ emulsion polymerization of waterborne poly (urethane-acrylate) (WPUA) nanoemulsions based on phase inversion process. The polymerizable surfmers containing terminal unsaturated double bonds (MSA-r) were successfully synthesized via catalytic chain transfer polymerization (CCTP). Random copolymer (MSAA) prepared through radical polymerization was utilized as control. The structure, surface tension and aggregation behavior of surfmers were characterized. The phase inversion, formation and stability of WPUA nanoemulsions were systematically investigated. Effects of MSA-r surfmer content and BMA/MMA ratio on the water resistance and thermal stability of the corresponding films were also discussed. It was found that the phase inversion mechanism of PUA prepolymer in the presence of MSA-r surfmers is different from conventional polyurethane prepolymer. The addition of MSA-r and MSA-t surfmers alters the rheological behaviors of PUA prepolymer via PUA-surfmer interactions, as well as the phase inversion process. Compared with WPUA/MSA-t emulsion, WPUA/MSA-r nanoemulsion displayed improved stability at higher solid content. The minimum particle size of WPUA/MSA-r nanoemulsion was 88.7nm and kept almost constant after 12-month storage, while the particle size of WPUA/MSA-t emulsion was 131.3nm and increased to 178.9nm. Moreover, the WPUA/MSA-r film possessed improved water resistance and thermal stability.