Fusion reactions on the cathode surface of glow discharge deuterium–deuterium fusion neutron sources contribute significantly to the neutron production rate (NPR). While the NPR shows a linear relationship with current in the low current regime, a rise in cathode temperature in the high-current regime causes stagnation of the NPR. This tendency may be caused by high-temperature-induced desorption of deuterium on the cathode. This study aims to clarify the relationship between NPR and deuterium desorption. The present study utilized a water-cooling system to prevent deuterium desorption on the cathode. A stainless-steel 304 cathode and a diamond-like carbon (DLC)-coated cathode were tested. The cooling system kept the cathode temperature below 315 K throughout the experiment. In the case of the DLC-coated cathode, the water-cooling system improves the NPR in a high-current regime (30 mA or more in the present study). At 50 kV and 60 mA, the NPRs were 1.87 × 106 and 8.39 × 105 (n/s), with and without water cooling, respectively. Furthermore, without the cooling system, the NPR correlation with the cathode temperature indicates good agreement with the estimation model of deuterium desorption on the DLC-coated cathode. This study demonstrates that suppression of deuterium desorption in the cathode improves NPR, especially in the high-current regime.