The invention relates to a cooling structure of a cylinder cover of a diaphragm compressor. According to most traditional water channel perforating manners, perforation is performed in the direction facing the insides of cylinder covers from the side walls of the cylinder covers, the heat exchange areas, passing central high-temperature zones, of water channels are very small, a lot of heat of thecentral high-temperature zones cannot be brought away timely, and the cooling effect is not obvious. The cooling structure of the cylinder cover of the diaphragm compressor comprises the cylinder cover; a cooling water groove is formed in the end surface of the cylinder cover and is formed inside the cylinder cover; an exhaust component is arranged on the cylinder cover; the cooling water groovesurrounds the exhaust component, communicates with a water inlet group and communicates with a water outlet group; the water inlet group is formed in the side surface of the cylinder cover; the wateroutlet group is formed in the side surface of the cylinder cover; a spiral ring is arranged in the water groove, so that cooling water flows sufficiently in the water groove, and a stagnant water zoneis prevented. The heat exchange area of the cooling water and the central high-temperature zone is increased, the heat of the central high-temperature zone is guided out, and the temperatures of thecylinder cover and exhaust are reduced.