The invention relates to the field of waterproof materials, and specifically discloses a preparation method of a cement-based waterproof material. The preparation method comprises the following steps:mixing water, ethanol and a silane coupling agent, and carrying out ultrasonic oscillation, thus obtaining an oscillation solution; grinding sodium bentonite, adding and mixing the sodium bentonite powder in a sodium hydroxide solution, carrying out ultrasonic oscillation, taking a suspension solution, preheating and stirring, dropwise adding the oscillation solution, stirring, refluxing, cooling, filtering, and washing, thus obtaining a washing product; mixing butyl acrylate, methacrylic acid and methyl methacrylate, thus obtaining a mixed solution; mixing water, sodium hydrogen carbonate and a composite emulsifying agent, dropwise adding the mixed solution, heating, adding organosilicone and an initiator, heating, cooling and filtering, thus obtaining emulsion; mixing the washing product with deionzed water, dropwise adding an ammonium persulfate-phosphoric acid water solution, stirring, adding the emulsion and a composite flame retardant, and uniformly stirring, thus obtaining a stirring solution; mixing the stirring solution, methyl hydroxyethyl cellulose ether and defoaming agent, stirring, adding cement under a stirring state, and uniformly stirring, thus obtaining the cement-based waterproof material.