The invention discloses a composite modified asphalt bridge deck waterproof bonding layer. The composite modified asphalt bridge deck waterproof bonding layer comprising a bonding lower layer, a bonding upper layer and a waterproof layer is characterized in that the bonding upper layer and lower layer are paved from epoxy modified asphalt of 0.4 kilogram per square metre; the waterproof layer is paved from thermoplastic elastomer modified asphalt of 0.6 kilogram per square meter; the epoxy modified asphalt is prepared, in proportion, from matrix asphalt, epoxy resin, curing agents, vulcanizingagents, curing accelerator, styrene butadiene rubber and talc; the thermoplastic elastomer modified asphalt is prepared, in proportion, from matrix asphalt, epoxidized natural rubber, thermoplastic elastomer, polyphenylene ether, and fiber. The composite modified asphalt bridge deck waterproof bonding layer has the advantages of making full use different characteristics of each material to enablethe waterproof bonding layer to have excellent bonding and waterproof properties, guaranteeing the epoxy modified asphalt to be in full bonding with a concrete bridge deck and an asphalt mixture surface layer, and avoiding various problems such as avoids problems such as waterproof layer breakage and flexural fatigue caused by base layer cracking stress transmitted to the waterproof layer, and premature aging under high stress by the thermoplastic elastomer modified asphalt.