The invention belongs to the technical field of wood coatings, and particularly relates to a special water-based varnish for outdoor wooden windows and a preparation method thereof. The special water-based varnish comprises the following components in parts by weight: water-based resin, a pH regulator, an antifoaming agent, a film-forming solvent, a wetting agent, a leveling agent, an antioxidant,a light stabilizer, a flatting agent, a preservative, a thickener and deionized water. In addition, the invention further provides specific preparation process steps of the special water-based varnish for the outdoor wooden windows. The special water-based varnish for the outdoor wooden windows has excellent anti-aging and anti-pulverization functions, good weather resistance and excellent adhesive force, water resistance and freezing resistance, and can be used for effectively protecting wood for a long time and prolonging the service life; the water-based varnish product obtained by the preparation method provided by the invention can achieve almost zero microbubbles in a tank, and the product prepared according to the process can achieve thick coating without bubbling in field construction.