The invention discloses a bottom filling adhesive having good compatibility with scaling powder and a preparation method thereof. The bottom filling adhesive is compounded by, by weight, 5-25 parts of self-synthesized compatible resin, 20-50 parts of epoxy resin, 5-20 parts of thinner, 1-3 parts of coupling agent, 0.1-1 part of dispersant, 35-50 parts of filler and 5-30 parts of curing agent, wherein the self-synthesized compatible resin is compounded by, by weight, 500-700 parts of dimer acid, 140-360 parts of hydroxyl-terminated toughened resin, 1-8 parts of methyl benzenesulfonic acid, 90-190 parts of low-viscosity bifunctional epoxy resin and 0.2-3.0 parts of triphenyl phosphine. Compared with the prior art, the compatibility with scaling powder of the bottom filling adhesive is excellent, the defects formed in the flowing and curing process are decreased, the flowing speed and the curing speed are high, the bottom filling adhesive meets the requirement for high density packaging, an expansion coefficient is small, and the reliability of packaging components is effectively guaranteed.