The invention provides a composite pavement sealing layer and a preparation method and application thereof and belongs to the technical field of road maintenance. The composite pavement sealing layerprovided by the invention comprises a bottom layer arranged on the surface of a to-be-treated road and a surface layer arranged on the surface of the bottom layer, wherein the bottom layer is formed by a normal temperature modified asphalt mixture which comprises asphalt, an asphalt modifier and aggregate; the surface layer is formed by a sand-containing fog seal layer mixture which comprises a waterborne concentrated cover material, an acrylic resin emulsion, fine sand and water; and the waterborne concentrated cover material comprises asphalt, emulsifier, argil and water. The composite pavement sealing layer provided by the invention has the beneficial effects that the softening point of the asphalt is reduced by utilizing the asphalt modifier, so that the mixing of the normal temperature modified asphalt mixture and the paving of the bottom layer can be realized under normal temperature conditions; and meanwhile, by utilizing the surface layer formed by the sand-containing fog sealing layer mixture, water on the road surface can be effectively prevented from sinking in road and damaging the bottom layer, so that the waterproof performance of the road surface is improved.