Morchella spp., precious edible and medicinal fungi with important economic and scientific value, have always attracted the attention of scientific researchers at home and abroad, while successful large-scale cultivation in multiple provinces has led to a northward shift of production regions. China's northward expansion of Morchella cultivation faces challenges from saline-alkali soils in arid regions. The purpose of this paper is to clarify the effects of Morchella cultivation on the saline-alkali soil of Ningxia, Northwest China. A comparative analysis was performed on the physical and chemical properties of soil, microbial community structure and function, and the abundance of functional genes encoding enzymes related to nitrogen metabolism in saline-alkali soils under three treatments:(1) an unplanted control (CK), (2) one cycle of Morchella cultivation (T1), and (3) two cycles of Morchella cultivation (T2). Morchella cultivation significantly contributed to the amelioration of saline-alkali soil, evidenced by a notable reduction in pH alongside enhanced soil nutrient content and enzyme activities. Metagenomic analysis further demonstrated that Morchella cultivation drove a structural remodeling of the soil microbial community, reshaping the genetic potential of soil nutrient cycling by altering the abundance of functional genes. Specifically, the first cultivation cycle initially suppressed core metabolic pathways, such as ABC transporters, carbon metabolism, and amino acid biosynthesis, while enriching pathways related to lipopolysaccharide biosynthesis and two-component systems for environmental adaptation. With extended cultivation and rotation, these fundamental metabolic pathways recovered and were re-enriched. Furthermore, Morchella cultivation appears to enhance the genetic potential for soil nitrogen metabolism, including denitrification, nitrogen assimilation, and nitrogen reutilization. However, cultivation also disrupted the microbial network responsible for phenolic acid degradation, manifested by an increased gene abundance of the synthesis key enzyme PAL, while the dominant microbial contributors to the degradation core enzyme P34O and its encoding genes pcaG/pcaH shifted from the original state (dominated by genera such as Arthrobacter) to a less efficient structure (dominated by Microvirga and Sphingomonas), ultimately leading to phenolic acid accumulation and the risk of hindering sustainable continuous cropping. This study highlights the extent of soil alterations induced by Morchella cultivation in saline-alkali environments and provides insights into the underlying microbial mechanisms.