The invention discloses a special waste rubber composite modifier for waterproof roll roofing and a preparation method of the special waste rubber composite modifier. The special waste rubber composite modifier is prepared from the following raw materials in parts by weight: 13 to 22 percent of waste rubber particles, 8 to 16 percent of polyaryletherketone, 6 to 10 percent of carboxylated polyisoprene and 40 to 63 percent of matrix asphalt. The preparation method of the special waste rubber composite modifier comprises the following steps: firstly, carrying out supercritical CO2 swelling and stirring preheating on waste rubber particles and then regenerating through a twin screw extruder to obtain liquid regenerated rubber; secondly, heating, melting and dehydrating the matrix asphalt, slowly raising the temperature to 210 to 265 DEG C, and then mixing the matrix asphalt with the liquid regenerated rubber to obtain rubber modified asphalt; thirdly, uniformly mixing the rubber modified asphalt with the polyaryletherketone and the carboxylated polyisoprene, carrying out preheating on a mixture, carrying out high-speed shearing by a colloid mill, then feeding a sheared product into a storage tank, and stably developing for a period of time. The special waste rubber composite modifier disclosed by the invention is used for products obtained from high-end waterproof roll roofing; combination properties of high and low temperature resistance, radiation resistance, tear strength and the like are greatly improved, and the waterproof property is excellent.