The invention discloses a paper flame retardant with a core-shell structure, which can be added into paste, solving the problem that flame retardants added into the paste in the prior art have adverseeffects on the performance of paperboards. The paper flame retardant is prepared from the following raw materials in parts by weight: 0.1-1 part of hydroxypropyl methyl cellulose, 5-10 parts of emulsifiers and 20-50 parts of flame retardant particles with core-shell structures; polyethyleneimine cross-linked products serve as shells of the flame retardant particles with the core-shell structures,and nano molecular sieves coated with ammonium polyphosphate serve as cores. The invention further discloses a preparation method and application of the paper flame retardant with the core-shell structure. The paper flame retardant can be uniformly dispersed in paper without affecting various properties of the paper, and the method is simple, and easy to operate.