A waterborne polyurethane-acrylate copolymer emulsion and a preparing method thereof are disclosed. The emulsion is prepared by preparing a phosphorus containing waterborne polyurethane emulsion containing carbon-carbon double bonds from diisocyanate, a flame-retardant polyol, a non-flame-retardant polyol, a chain extender containing an acidic group, hydroxyl acrylate and an end-capping agent through a chemical grafting method; and then subjecting acrylate, phosphate containing a carbon-carbon double bond, vinyl silicone oil, a vinyl silane coupling agent and an acrylic acid type crosslinking agent which are adopted as raw materials to emulsion polymerization under protection of a phosphate surfactant. The copolymer emulsion has a high solid content, time for drying the copolymer emulsion is short, and a product after the copolymer emulsion is dried has good flame retardance and resistance to thermal decomposition.