The invention provides nano SiO2 high-strength waterproof impermeable mortar and a preparation method thereof. The waterproof impermeable mortar is prepared from the following raw materials: cement, water, sand, fly ash, nano SiO2 dispersion liquid and the like. By adding other active materials such as the nano SiO2, the polypropylene fibers and the early strength agent, the cement-based material can be brought into pores inside the cement-based material under the carrying action of water, particularly capillary pores with small sizes, to absorb water and expand, so that a filling effect is achieved. Besides, nano SiO2 can participate in and promote hydration reaction, and produced fine and regular hydrated crystalline substances are attached to the peripheries of pores, so that the microstructure is densified, a dense impermeable area is formed in the deep position of the interior of the cement-based material, and the waterproof and impermeable performance of the cement-based material is greatly improved. The added nano SiO2 can improve the microstructure of the cement-based material and inhibit the generation of cracks, so that the strength, seepage resistance and durability of the cement-based material are improved.