The invention relates to a cement-based penetrable crystallized waterproof paint, a preparation method and a construction method thereof. The cement-based penetrable crystallized waterproof paint is prepared from the following raw materials in percentage by weight: 65 to 70 percent of cement, 3 to 10 percent of modified bentonite, 2 to 5 percent of modified sodium silicate, 1 to 5 percent of diffusant, 0.5 to 1 percent of penetrant, 2 to 10 percent of wollastonite and 15 to 25 percent of quartz sand. The waterproof paint can recover minute cracks on concrete interfaces and inhibit the water seepage and damp of base interfaces effectively. In addition, the waterproof paint is high in capacity of freezing resistance, high-temperature resistance, chloridion resistance and acid and alkali resistance, and has a long waterproof effect. According to the cement-based penetrable crystallized waterproof paint, leveling layers on the concrete interfaces are saved, and protective layers are savedafter the concrete interfaces are coated, so the waterproof construction is simple. The cement-based penetrable crystallized waterproof paint is suitable for constructional engineering such as underground engineering, subway tunnels, civil air-defense construction, water ponds, oil sumps, sewage tanks, barns, bathrooms, roof squares, parking platforms, high-grade roadways and the like, and is used for processing defects of cracks, honeycomb pitted surfaces and the like of the concrete interfaces.