The invention discloses a high-performance thermosetting epoxy asphalt binder, comprising a part A component and a part B compound, wherein the part A component comprises 100 weight parts of epoxy resin, 20-35 weight parts of flexibilizer, 0.5-2 weight parts of promoter, and 8-20 weight parts of diluent; the part B component comprises 300-350 weight parts of asphalt, 150-160 weight parts of flexible curing agent, 10-15 weight parts of promoter, 2-5 weight parts of compatilizer, and 100 weight parts of diluent; and the ratio of the part A component to the part B component is 100:350-440. According to the invention, by using flexible long-chain fatty acid anhydride as the curing agent and carrying out solidification reaction on the curing agent with the epoxy resin, a stereo cross-linked structure is formed, and the bonding capability and water resistance of asphalt are increased; by using liquid rubber as the flexibilizer, the flexibility of the epoxy asphalt binder is raised to adapt to the flexibility of a steel plate, and by prereacting the flexibilizer with epoxy resin firstly for grafting, the compatibility between the epoxy asphalt binder and asphalt is raised. The epoxy asphalt binder is suitable for bonding and waterproofing of steel bridge floor, cement concrete bridge floor, tunnel, highway and other pavements. The invention also discloses a preparation method of the epoxy asphalt binder.