Abstract:[Background] Since Morchella was successfully cultivated for commercial purposes, soil and soil problems caused by continuous cultivation have become obstacles in the sustainable development of Morchella. [Objective] To offer a reference point for soil improvement and ecological restoration in the cultivation of Morchella. [Methods] During the harvest stage, soil samples were collected from both wild habits of Morchella and the cultivation regions of Morchella with different yields. The physicochemical properties and microbial communities of these samples were then analyzed. [Results] The content of nitrogen and activities of alkaline and neutral phosphatase, catalase, and urease in the soil samples from wild habitats were all higher than those from cultivation areas. The relative abundance of bacteria in the rhizosphere soil of Morchella was significantly higher than that of fungi. The richness and interrelations of microorganisms in the soil samples from wild habitats were much higher than those from cultivation areas. At the bacterial phylum level, Actinomycetota, Proteobacteria, Chloroflexota, Acidobacteriota, and Bacteroidota accounted for more than 80%. The soil samples from cultivation areas of Morchella had higher abundance of Firmicutes than those from wild habitats, which reached up to 28.91% in low-yield areas. At the fungal phylum level, Ascomycota, Basidiomycota, and Mortierellomycota accounted for 90% or more. The dominant genera were Bacillus and Mortierella in the low-yield areas and Humicola and Aspergillus in high-yield areas. Moreover, the yield, alkaline phosphatase, urease, and catalase showed significantly positive correlations with several bacterial and fungal genera. [Conclusion] Abundant organic matter and microbial communities are conducive to the yield improvement, ecological restoration, and sustainable development of Morchella.