The invention relates to a frustule asphalt modifier, a frustules asphalt modifier modified composite asphalt, and a preparation method of the frustules asphalt modifier. The frustules asphalt modifier is prepared from, by weight, 5 to 20 parts of frustule, 10 to 25 parts of waste rubber powder, 0 to 5 parts of petroleum resin or low grade asphalt, and 0 to 3 parts of a stabilizing agent. The invention also discloses a frustules composite modified asphalt, and a preparation method thereof. The frustule asphalt modifier is capable of improving the high temperature performance, the low temperature performance, the fatigue resistance, and the water stability of asphalt mixtures; the obtained frustules composite modified asphalt possesses excellent heat storage stability, and low temperature crack resistance, and is capable of prolonging the service life of road. A part of expensive SBS is replaced by cheap frustule, compared with the pavement performance of modified asphalt prepared via using of only SBS, the pavement performance is improved, and modified asphalt cost is reduced.