The invention discloses a water-based inorganic silicon-organic silicon-polyurethane adhesive and a preparation method thereof. The adhesive consists of a water-based adhesive component A and a curing agent component B, wherein the water-based adhesive component A is obtained by synthesizing 55 to 90 parts of silica sol, 12 to 20 parts of organosilane, 120 to 200 parts of polyol, 15 to 25 parts of polyisocyanates, 3 to 5 parts of emulsifying agent, 0.5 to 1.2 parts of catalyst, 80 to 150 parts of powder, and 900 to 1,200 parts of deionized water; the curing agent B is one or mixture of more than one of methylene diphenyl diisocvanate (MDI), polyaryl polymethylene isocyanate (PAPI), and hexamethylene diisocyanate (HDI); and during use, the curing agent component B and the water-based adhesive component A are uniformly mixed in a mass ratio of (5-15):100. The adhesive prepared by the method has high adhesive strength and water resisting property on wood, and the preparation process is simple and low in cost.