The invention discloses double-layer composite fuel filter paper coated with a nanometer silver ion carried antibacterial agent, and a preparation method thereof. The double-layer composite fuel filter paper is characterized by being prepared from the following raw materials in parts by weight: 1 to 3 parts of tencel fiber, 10 to 20 parts of broad leaf wood pulp fiber, 1 to 2 parts of hydroxymethyl cellulose, 10 to 20 parts of coniferous pine wood pulp fiber, 10 to 20 parts of polyester fiber, 10 to 20 parts of sepiolite nanofiber, 3 to 5 parts of Fe2O3, 5 to 10 parts of TiO2, 4 to 8 parts of MgO, 25 to 35 parts of silane coupling agents KH560, a proper amount of nanometer silver ion carried antibacterial agents, 15 to 20 parts of polyoxyethylene water solutions, 2 to 4 parts of titanate coupling agents DNZ201, 50 to 60 parts of isopropanol, 5 to 10 parts of styrene-acrylic emulsion and a proper amount of polyacrylate emulsion. The gap between layers is improved; meanwhile, the obvious porosity gradient is reserved; the filtering efficiency is improved; Fe2O3 and TiO2 have an oxygenolysis effect on organic matters and inorganic matters in automobile exhaust; the nanometer silver ion carried antibacterial agent is used for coating the surface of the filter paper, so that the filter paper has efficient sterilization and bacteriostasis performance.