The invention provides a water-borne woodware coating containing a modified polyurethane emulsion and a preparation method thereof. The water-borne woodware coating is composed of the following components: water, a thickening agent, a defoaming agent, a pH regulator, an antifreezing agent, a film-forming auxiliary agent, the modified polyurethane emulsion, a levelling agent, a nano inorganic antibacterial aldehyde removing agent, and water-borne paint inorganic hardening resin. The selected modified polyurethane emulsion includes a self-crosslinkable polyurethane acrylate composite emulsion, a core-shell interpenetrated network-structure polyurethane acrylate copolymer emulsion, a silane coupling agent modified polyurethane acrylate composite emulsion, and an epoxy resin modified polyurethane emulsion. The plurality of emulsions are added to the water-borne woodware paint, and thus the coating has the properties of high hardness and adhesion force, and good water resistance, alcohol resistance and pollution resistance; the selected nano inorganic antibacterial aldehyde removing agent has the effects of environmental protection, safety, no toxicity, and long-term bacterial resistance; and the selected water-borne inorganic hardening resin is used for improving the hardness, the adhesion force and the chemical resistance of the water-borne paint.