The invention belongs to the field of materials, and discloses a flame retardant having reactivity and adopting a core-shell structure as well as a preparation method and an application of the flame retardant. The flame retardant takes APP (ammonium polyphosphate) as a capsule core and takes a methyl methacrylate and hydroxyethyl acrylate copolymer as a capsule material. The preparation method comprises the following steps: APP particles are added to a solvent at the room temperature, stirred and heated to 50-60 DEG C; a polymer monomer is added dropwise while stirred, the mixture is stirred for 10-20 min at the temperature of 50-60 DEG C and then heated to 70 DEG C, and a benzoyl peroxide solution is added dropwise; the mixture is heated to 75-85 DEG C, subjected to heat preservation and stirred for reacting for 4-8 h, and the flame retardant having reactivity and adopting the core-shell structure is obtained after extraction filtration, washing and drying. The surface of the flame retardant contains active reaction groups (hydroxyl) which can react with polymer such as rigid polyurethane foam, flexible polyurethane foam, polyurethane elastomer, polyurea and the like, so that the compatibility of the flame retardant in a substrate is improved, and the flame retardant is insoluble in water and has efficient flame retardancy.