The invention relates to a fluorine-silicon modified waterborne alkyd resin and a preparing method thereof. The fluorine-silicon modified waterborne alkyd resin is prepared from vegetable oil fatty acid, organic acid anhydride, polyol, fluorinated allyl monomers, isocyanate, hydroxyl-terminated organic silicon, acrylic monomers and deionized water. Single-component waterborne paint, double-component waterborne paint and room-temperature curing paint can be blended with the fluorine-silicon modified waterborne alkyd resin prepared through the method. The prepared fluorine-silicon modified waterborne alkyd resin has the performance such as high adhesion, stain resistance, high hardness, water resistance, durability, hydrophobicity and self-cleaning performance, and can be widely applied to waterborne wood paint, waterborne industrial paint, waterborne anti-fouling paint, waterborne corrosion resistance paint, waterborne special engineering paint such as radar dome materials, wind power generation, nuclear power and vessel paint and the like.