The invention discloses waterborne two-component varnish and a preparation method thereof. The waterborne two-component varnish is formed by mixing a component A and a component B in the mass ratio of(2.5-3.5):1, wherein the component A comprises, by weight, 25-40 parts of waterborne acrylic resin, 25-40 parts of waterborne polyester resin, 0.1-1 part of base material wetting agent, 0.1-1 part offlatting agent, 0.1-1 part of defoaming agent, 0.1-1 part of ultraviolet absorbent, 0.1-1 part of bactericide, 5-10 parts of cosolvent, 0.1-1 part of thickening agent and 2-5 parts of carboxymethyl chitosan; the component B comprises, by weight, 40-60 parts of isocyanate curing agent, 0.1-1 part of adhesion promoter and 40-60 parts of cosolvent. The fullness, glossiness, flatting property, construction performance and mechanical properties of the varnish can reach the standards of high-performance oily varnish and are higher than those of existing waterborne varnish, and the varnish has the advantage of being low in content of VOCs.