The invention discloses a novel moisture-curing flame-retardant polyurethane hot melt adhesive and a preparation method thereof. The novel moisture-curing flame-retardant polyurethane hot melt adhesive is characterized by being prepared from 1-20 parts of polyether diols, 1-35 parts of liquid polyester diols, 1-40 parts of flame-retardant polyether glycol, 1-35 parts of crystalline polyester diols, 1-35 parts of an isocyanate-containing modified polyacrylic acid fluorosilicone copolymer, 1-50 parts of isocyanate, 0.01-1 part of a catalyst, 0.01-1 part of an antioxidant and 0.1-2 parts of a silane coupling agent. The isocyanate-containing modified polyacrylic acid fluorosilicone copolymer is synthesized firstly, the chemical structure of the copolymer is poly(hexafluorobutyl acrylate-random-monomethacryloxypropyl terminated polydimethylsiloxanes-random-methyl acrylate-random-isocyanatoethyl methacrylate, the copolymer is added to a polyurethane prepolymer and subjected to condensation polymerization, a fluorosilicone-containing acrylate copolymer chain segment and a reaction type flame retardant are introduced and have an efficient synergistic effect, and therefore, comprehensive chemical resistance, oil resistance, water resistance and flame retardance are improved.