Alfalfa (Medicago sativa L.) is an important forage legume in farming and animal husbandry systems. In this study, MiSeq high-throughput sequencing was applied to assess the relationship between bacterial and fungal community structures and alfalfa growth characteristics and soil physical and chemical properties induced by different cultivars alfalfa (Victoria, Kangsai, Aohan) in the grey desert soil. The results showed that the diversity of bacterial and fungal in Victoria was higher, and the bacterial diversity was significantly lower for alfalfa with Aohan than for the others, and the fungal diversity was lower for alfalfa with Kangsai than for the others. Heatmap showed that total nitrogen, fresh weight, pH and organic have significantly affect fungal community structure, whereas pH and organic carbon also significant effects on bacterial community structure. LefSe analysis showed that the growth adaptability of introduced alfalfa is mainly related to fungal and bacterial species, and the beneficial microorganisms with significant differences and relative high abundance are significantly enriched in Victoria. Pathogens with high relative abundance are mainly concentrated in Aohan alfalfa soil. Based on our findings, Victoria is the high-yield alfalfa suitable for planting in gray desert soil, while planting Kangsai and Aohan alfalfa needs probiotic for adjuvant.