The invention discloses a preparation method of a high-impact-resistant waterproof type epoxy resin toughening agent, and belongs to the technical field of preparation of toughening agents. The methoddisclosed by the invention is characterized in that butyl acrylate, 1,4-butanediol diacrylate, allyl methacrylate, distilled water, sodium dodecyl benzene sulfonate and potassium persulfate are subjected to heating reaction to prepare a home-made seed emulsion, and the home-made seed emulsion is mixed with butyl acrylate, methyl methacrylate, a cross-linking agent, an emulsifying agent, an initiating agent and a grafting agent together to prepare a core layer emulsion and a shell layer emulsion; divinyl benzene is an oil-soluble initiating agent and mainly swells in emulsion particles, and only a small amount of divinyl benzene is dissolved in a water phase, thereby improving the impact-resistance strength of the toughening agent; and nano silicon dioxide is added to a polyacrylate emulsion with better water resistance and physical and mechanical properties to enable the polymer to have high water absorbing capacity, and resin can be cured in a humid environment or even underwater andcan keep good water resistance, thereby improving the water resistance of the toughening agent.