The invention discloses a complex modified asphalt composition which is composed of the following constituents by weight: 55%-89% of matrix asphalt of which the mass content of asphaltene is more than 8%, 2%-8% of styrene-butadiene block polymer, 4%-16% of active adhesive powder, 0.1%-1% of stabilizer and balance of blending component. The invention also discloses a method for preparing the complex modified asphalt composition. The complex modified asphalt provided by the invention is excellent in various indexes and high in compatibility, and the separation softening point difference is less than 2 DEG C. Compared with the prior art, the technical scheme of the invention has the following advantages: the thickened oil asphalt with high asphaltene content previously considered as being not suitable for being used as the raw material is used in the invention, so that the range of raw material for the modified asphalt is expanded; and the environmental-friendly active adhesive is added to replace the expensive SBS, and more attention is paid to environment protection while the cost is lowered.