The invention discloses a waterproof connecting structure of a deformation joint of a building roof. The waterproof connecting structure comprises a waterproof roll layer, a fireproof rock wool layer,a waterproof elastic material connecting band, an elastic rubber band, the deformation joint and a waterproof aluminum plate. The deformation joint is arranged between a first concrete wall body anda second concrete wall body. The fireproof rock wool layer, the waterproof roll layer and the waterproof aluminum plate are sequentially laid on the top of the deformation joint from bottom to top. Prefabricated grooves are formed in the first concrete wall body and the second concrete wall body on the two sides of the deformation joint, pre-embedded anchor cables are arranged in the first concrete wall body and the second concrete wall body, locking heads are fixed into the pre-embedded anchor cables and connected with locking plates, the locking plates are arranged in the prefabricated grooves, bolt holes are formed in the locking plates, connecting bolts penetrate into the bolt holes, and the connecting bolts sequentially penetrate through clamping arms, the bolt holes of the locking plates, cushion plates and U-shaped glands from top to bottom to be connected with nuts. Assembly and disassembly are convenient, mounting and replacing of the fireproof elastic material connecting bandor the elastic rubber band are convenient, and operation is convenient.