The inadequate ability to dissipate heat of the gas head cover of the diaphragm compressor will result in its excessive temperature, which will put the operation of the hydrogen filling station at risk for safety issues and raise operating costs. This paper analyzed the structure and the heat transfer characteristics of the gas head cover, along with the relevant heat transfer boundaries, based on which a finite element simulation model of the temperature distribution was established. A test rig for the temperature test of a 22 MPa diaphragm compressor was built to validate this simulation model. The results indicated that the simulated temperatures agree well with the measured values, and the deviation is within 9.1%. Further, this paper proposed two head cover structures for enhancing the heat transfer according to the temperature field distribution characteristics, and the simulation and experimental verification were carried out, respectively. The findings demonstrate that the method of enhancing heat transfer around the centre area is more effective, reducing the highest temperature by 14.1 °C, because it greatly lowers thermal conduction resistance, which is the principal impediment to the heat dissipation of the gas head cover.