The work aims to prepare acrylate modified waterborne polyurethane emulsion and study the effects of inner-crosslinking agent on the performances of such emulsion. The waterborne acrylate-polyurethane (WPUA) was prepared with polyurethane as the seed emulsion, trimethylolpropane monoallyl ether (TMPME) as the chain extender and intramolecular crosslinking agent, and methyl methacrylate (MMA) and butyl acrylate (BA) as the acrylate monomer. The effects of dosage of TMPME on the properties of the emulsion film were studied. The water absorption of the emulsion film could be reduced to 7.0% when the mass fraction of TMPME was 3%. In addition, heat treatment was beneficial to improve the water resistance of emulsion film. The tensile strength of emulsion film could be increased to 8.7 MPa and the elongation at break can be increased to 620% when the mass fraction of TMPME was 2%. At this time, the comprehensive performance was the best. The introduction of a certain amount of TMPME can improve the molecular crosslinking degree and film compactness in WPUA, thus significantly improving the water resistance and mechanical property of the emulsion film.