The invention discloses inorganic-organic composite modified cross-linking aqueous polyurethane emulsion and a preparation method thereof. The preparation method comprises the following steps that step 1, polyester polyols and diisocyanate are mixed, and a catalyst dibutyltin dilaurate is dropped, and then nitrogen is introduced for reaction; step 2, then a hydrophilic chain extender is added forreaction, then furan resin is added for reaction; step 3, after a neutralization agent is added for reaction, water is added for dispersion, and aqueous polyurethane emulsion is obtained; and step 4,nano SiO2 is added to the aqueous polyurethane emulsion, and dispersion emulsification are carried out in a ultrasonic reactor, and after the reaction is completed, a solvent is removed, and the cross-linking aqueous polyurethane is obtained. According to the inorganic-organic composite modified cross-linking aqueous polyurethane emulsion and the preparation method thereof, furan resin chain segments are introduced into polyurethane chain segments, and a Diels-Alder reaction is carried out between double bonds on a furan ring, so that the mechanical property of the cross-linking aqueous polyurethane are improved; and the nano SiO2 is introduced, and the cross-linking density of a polymer coating is increased, so that space shrinked water molecules are difficult to enter, and the water resistance is improved.