To investigate the effects of different soil types on the rhizosphere fungal community structure of alfalfa (Medicago sativa L.) and their driving mechanisms, a pot experiment was employed to systematically compare the response differences in root morphology, soil chemical properties, and rhizosphere fungal community structure of alfalfa seedlings grown in aeolian sandy soil and saline-alkaline soil from western Jilin Province. The results indicate that, compared to aeolian sandy soil, saline-alkaline soil significantly inhibits alfalfa root growth. The reductions in root parameters follow the order: root volume, root surface area, root length, and root tip number, with root volume showing the most substantial decrease. Although the soil pH under saline-alkaline conditions is significantly lower, the contents of available nitrogen, available phosphorus, available potassium, total nitrogen, and total phosphorus are all significantly higher than those in the aeolian sandy soil. At the phylum level, the rhizosphere fungal communities in both soil types are primarily dominated by Ascomycota, Basidiomycota, and Mortierellomycota. The fungal diversity index significantly increases in the soda saline soil, while the community coverage index decreases. Correlation analysis reveals that the relative abundance of Ascomycota shows a significantly positive correlation with soil available nitrogen. In contrast, the relative abundance of Basidiomycota is negatively correlated with soil pH and available nitrogen but positively correlated with soil organic carbon. The relative abundance of Mortierellomycota exhibits a significantly positive correlation with soil organic carbon. In conclusion, the composition and diversity of the rhizosphere fungal community recruited by alfalfa differ significantly under different soil conditions. This variation is primarily regulated by key soil environmental factors, including pH, available nitrogen, and organic carbon.