The shitake mushroom (lentinula edodes) industry in the Gobi Desert region of southern Xinjiang has experienced rapid development and has reached a certain scale. To clarify the laws governing different cooling methods in greenhouses and identify suitable cooling methods for mushroom production in the Gobi Desert region, this study focused on monitoring the environmental changes in greenhouses using three different cooling methods: natural ventilation cooling, water-sprinkling roof cooling, and a fan and pad cooling system. The results showed that when combined with external shading (shade netting), natural ventilation cooling, fan and pad cooling, and water-sprinkling roof cooling, respectively, reduced the air temperature by 8.6 °C, 14.0 °C, and 15.2 °C. They also increased the relative humidity by 15.3%, 43.3%, and 51.2%, resulting in cooling efficiencies of 28.5%, 56.3%, and 68.1%, respectively. The water-sprinkling roof cooling system demonstrated the best cooling effect and temperature uniformity and had higher economic benefits. Therefore, the use of the external sprinkler cooling method in double-skeleton greenhouses is suitable for summer lentinula edodes production in the Gobi Desert region of southern Xinjiang.