The invention relates to an acrylic ester modified epoxy bottom filling material and a preparation method thereof. The acrylic ester modified epoxy bottom filling material is prepared by adding low-viscosity epoxy resin, a reactive diluent, a latent curing agent, an acrylic ester monomer, an initiator and a polymerization inhibitor serving as raw materials into a stirring container, respectively, uniformly mixing in a vacuum state, and discharging out the material, thereby obtaining a product. The bottom filling material provided by the invention is high in flowing speed at the room temperature, high in curing speed and good in storage stability, can be repaired, and can be widely used in inverted chip processes.