The invention discloses a preparation method of an aqueous polyurethane-acrylate emulsion, wherein the aqueous polyurethane-acrylate emulsion is obtained by chemical bonding of polyurethane as a shell and acrylate as a nucleus; the preparation method of the aqueous polyurethane-acrylate emulsion comprises the steps of using polyether glycol, isocyanate and an assistant to prepare a disulfide ester-terminated polyurethane pre-polymer shell layer; enabling the pre-polymer and acrylate monomer to react to obtain a nucleus; mixing the nucleus with water, and obtaining the water dispersible emulsion; due to the controllable polymer with the emulsion structure, molecule weight, molecular weight distribution, micelle shape and formed by the shell and the nucleus, the water resistance, low-temperature film-forming performance and the gloss can be improved, so that the emulsion has wide application in fields such as coatings, adhesives, inks, leather fabric coating agents and the like.