The invention belongs to the technical field of adhesives, and particularly relates to a preparation method of a flame-retardant and waterproof adhesive for a corrugated carton. The preparation methodspecifically comprises the following steps: (1) an organic silicon modified emulsion is prepared; (2) a white prepolymer emulsion is prepared; (3) an acrylic modified flame-retardant organic siliconemulsion is prepared; and (4) 110-120 parts of the acrylic modified flame-retardant organic silicon emulsion is put into a high-speed mixer, 1.5-2.3 parts of carnallite powder, 24-27 parts of polyhalite powder and 5-7 parts of a flame retardant are added, even stirring and mixing are conducted, and then the flame-retardant and waterproof adhesive is obtained. The prepared adhesive is transparent,high in adhesion and good in stability, water-based adhesive bonding, quick drying, and acid and alkali resistance are achieved, no organic solvent is contained, the poisonless, tasteless, non-combustible, environment-friendly and pollution-free effects are achieved, and pollution-free production can be achieved. The flame-retardant and waterproof adhesive is suitable for the carton not coated andpolished, and the corrugated carton is protected very well.