The invention belongs to the technical field of building construction materials and preparation of the building construction materials, and relates to a silica sol-silane emulsion capillary crystalline waterproof material and a preparation method thereof. The preparation method comprises the following steps: at first, mixing silica sol, silane emulsions, silane coupling agents, stabilizers, isopropanol, tartaric acid and coalescing agents, controlling the temperature to 50-70 DEG C, stirring all the time, sufficiently reacting for 4-8 h, cooling, and then regulating the pH value to 3.5-5.5 with phosphoric acid, wherein the weight percentage of the silica sol, the silane emulsions, the silane coupling agents, the stabilizers, the tartaric acid and the coalescing agents are respectively 10%-60%, 20%-70%, 5%-15%, 1%-3%, 0.08%-0.5% and 1%-3%; at last, adding water to enable the weight percentage to 100% to obtain the silica sol-silane emulsion capillary crystalline waterproof material. The preparation process is simple, the cost is low, the water-proof effect is good, and the waterproof material is environment-friendly.