The invention discloses a tunnel top waterproof structure and an implementation method thereof, and belongs to the technical field of building waterproof. The tunnel top waterproof structure comprisesa concrete layer, a waterproof material layer, a structural supporting layer and bolts for fastening the layers. The waterproof material layer and the structural supporting layer adopt a splicing prefabricated type, the splicing gap of the waterproof material layer and the contact surface between the layers and the bolts are subjected to waterproof treatment, and thus the problem of water permeating from the contact gap is solved; and the waterproof material adopts layered and integrated types, multiple waterproof is achieved, and a main material of the waterproof material is a flexible material, so that the problem of water leakage caused by cracking or deformation of the concrete layer is effectively solved.