The invention relates to a highly weather-resistant protective agent for external-wall stones and a preparation method of the protective agent. The materials comprise deionized water, silicone acrylic emulsion, a silicyl fluorinated copolymer solution, a coalescing agent, an ultraviolet light absorber, a wetting agent and an antifoaming agent. The protective agent is prepared by blending a low-cost silicon-acrylic film-forming protective agent silicone acrylic emulsion and an expensive fluorosilicone penetrating type protective agent silicyl fluorinated copolymer solution which serve as main raw materials. The prepared protective agent is moderate in cost, simple in preparation method and convenient to use; a complete film layer is formed on the stone surface by virtue of the silicone acrylic emulsion, water is prevented from entering the stone gaps, the silicyl fluorinated copolymer solution can permeate into the stone gaps, and the way of allowing Ca(OH)2 to enter the stones is further cut off. The protective agent disclosed by the invention is high in weather resistance, does not yellow and discolor even if being positioned in ultraviolet irradiation for a long time, has excellent light retention and color retention performances and is suitable to be exposed on outdoor stones for a long time, and the service life of stone exterior facade can be greatly prolonged.