The invention relates to a waterproof vibration-damping type asphalt concrete grade crossing pavement structure, which comprises an asphalt mattress and a graded broken stone layer sequentially arranged on a foundation in a crossing area from bottom to top. Base layers are arranged on areas from two sides of the graded broken stone layer to a road adjacent to the crossing; a concrete sleeper is paved on the graded broken stone layer; a track is paved on the concrete sleeper; concrete layers are casted outside areas from two sides of the concrete sleeper to the crossing; asphalt surface layersare paved on the concrete layers and the base layers. A pavement method of the waterproof vibration-damping type asphalt concrete grade crossing pavement structure comprises the following steps of disassembling an old crossing pavement, compacting the foundation, paving the asphalt mattress, paving the graded broken stone layer, paving the base layers, paving the concrete sleeper, installing the track; casting the concrete layers, paving the surface layers, and finishing construction. The waterproof vibration-damping type asphalt concrete grade crossing pavement structure and the pavement method thereof provided by the invention have the beneficial effects of capability of remarkably improving a carrying capacity and the durability of a road-rail grade crossing, and quick and convenient construction process.