Morchella is a kind of precious edible, medicinal fungi with a series of important effects, including anti-tumor and anti-oxidation effects. Based on the data of 18 environmental variables and the distribution sites of wild Morchella species, this study used a maximum entropy (MaxEnt) model to predict the changes in the geographic distribution of Morchella species in different historical periods (the Last Glacial Maximum (LGM), Mid Holocene (MH), current, 2050s and 2070s). The results revealed that the area under the curve (AUC) values of the receiver operating characteristic curves of different periods were all relatively high (>0.83), indicating that the results of the maximum entropy model are good. Species distribution modeling showed that the major factors influencing the geographical distribution of Morchella species were the precipitation of the driest quarter (Bio17), elevation, the mean temperature of the coldest quarter (Bio11) and the annual mean temperature (Bio1). The simulation of geographic distribution suggested that the current suitable habitat of Morchella was mainly located in Yunnan, Sichuan, Gansu, Shaanxi, Xinjiang Uygur Autonomous Region (XUAR) and other provinces in China. Compared with current times, the suitable area in Northwest and Northeast China decreased in the LGM and MH periods. As for the future periods, the suitable habitats all increased under the different scenarios compared with those in contemporary times, showing a trend of expansion to Northeast and Northwest China. These results could provide a theoretical basis for the protection, rational exploitation and utilization of wild Morchella resources under scenarios of climate change.