The invention discloses a waterborne acrylate adhesive powder with a core-shell structure and a preparation method thereof. The preparation method comprises the following steps of firstly, adding an emulsifier into water; then, adding a soft monomer, a hard monomer and a functional monomer, uniformly mixing, and magnetically stirring, so as to form a pre-emulsifier; heating to 75 to 80 DEG C, adding a buffer solution into a reactor, dripping 20 to 50% of pre-emulsifier by mass and 1 / 2 to 3 / 4 of initiator by mass under the N2 (nitrogen) atmosphere, and stirring to react, so as to prepare a primary emulsifier; after warming, dripping the left initiator and pre-emulsifier, adding a chain transfer agent, warming for 1 to 2h after the dripping is finished, cooling, and discharging the material;adding a coupling agent, nanometer calcium carbonate or SiO2 (silicon dioxide) and a polyvinyl alcohol water solution, dispersing, treating by ultrasonic waves at room temperature, spraying, and drying. The waterborne acrylate adhesive powder has the advantages that the environment-friendly and non-toxic effects are realized; the adhering property is guaranteed, and the good water-resistant property is realized; the waterborne acrylate adhesive powder can be used under the complicated and precise conditions; the production cost is low, the operation is simple, and the required time is short.