The invention discloses a crystalline self-repairing polymer cement-based waterproof material and a preparation method thereof. The crystalline self-repairing polymer cement-based waterproof materialis prepared from the following raw materials in percentage by mass: 27 to 35 percent of Portland cement, 18 to 24 percent of quartz sand, 0.8 to 1 percent of vinyl silane coupling agent, 6 to 9.5 percent of an excitant, 0.2 to 0.5 percent of an ultraviolet light absorber and 30 to 48 percent of modified polyacrylate emulsion, the preparation method of the modified polyacrylate emulsion comprises the following steps: I, weighing; II, adding an acrylate monomer and methacrylic acid into ethanol, stirring and dissolving to obtain a solution A; III, adding sodium itaconate, sodium p-styrenesulfonate, tetrasodium iminodisuccinate and an initiator into deionized water, and stirring for dissolving to obtain a solution B; and IV, uniformly mixing the solution A and the solution B, transferring into a reaction kettle, and carrying out copolymerization reaction at 70-100 DEG C for 3-6 hours, thereby obtaining the product. According to the invention, structures such as -COONa and -SO3Na are introduced into a copolymer to form a copolymer emulsion with a chelating effect and an emulsifying and dispersing effect, so that a modified polyacrylate-concrete stably combined compact waterproof layeris formed.