The invention relates to a method for preparing a flame-retardant core-shell type waterborne acrylate resin coating. The method comprises the following steps of adding water, an emulsifier and acrylic acid, raising the temperature to 40 DEG C, stirring for 30 minutes, adding a monomer A, emulsifying for 15-45 minutes, raising the temperature to 70 DEG C, starting to introduce recirculation water, raising the temperature to 80 DEG C, reacting for 2 hours, dropwise adding an initiator for 2-4 hours, and reacting for 1-2 hours; adding manganese amino acid, stirring and reacting for 1-4 hours at 80 DEG C, adding a metal salt to adjust the pH value to be 4, adding manganese acetate, stirring and reacting for 1-2 hours at 60 DEG C to obtain a core layer emulsion; simultaneously dropwise adding a monomer B and an initiator into the core layer emulsion for 1-3 hours, stirring and reacting for 3 hours at 70-85 DEG C, adding a crosslinking agent, reacting for 1-3 hours at 70-90 DEG C, cooling to 40 DEG C, adding molybdenum di(2-ethylhexyl)phosphorodithioate and an emulsifier, reacting for 40 minutes, adding the material B, stirring and reacting for 1-3 hours at 65-85 DEG C and adding aqueous ammonia to adjust the pH value to be 7-8 to obtain the flame-retardant core-shell type waterborne acrylate resin coating. By virtue of the preparation method, the flame resistance of the acrylate resin can be greatly improved and the shortcoming of yellowing of a traditional acrylate resin film can also be improved.