<p>The continuous cropping of garlic leads to reduced yield and quality of serious soil diseases. This study aimed to find suitable rotation-fallow systems to break the bottleneck of continuous cultivation of purple garlic by improving the soil properties and microbial communities. In this study, three rotation systems (one constant, one rotation, and one fallow system) were implemented by field trials, and the comprehensive analysis was performed by assessing garlic yield, soil physicochemical properties, enzyme activity, and overall microbial composition. Proteobacteria, Acidobacteria, Bacteroidetes, Planctomycetes, Gemmatimonadetes, and Actinobacteria were the dominant bacteria phyla with a respective relative abundance 5.0% or more, and Ascomycota, Mortierellomycota, Basidiomycota and Chytridiomycota were the dominant fungal phyla with a respective relative abundance 1.0% or more in three treatments. Based on the results of redundancy analysis (RDA), soil carbon (SC), available potassium (AK), phosphatase, and pH were the main soil factors that affect the abundance structure of bacteria by different rotation tillage systems. Cropping rotation with <i>Vicia sativa</i> (V. sativa) can alleviate the continuous cropping barrier and improve garlic yield with significant effects on soil physicochemical properties, enzyme activity, and diversity of soil microbial communities. The results of this study provided beneficial theoretical guidance for the bioremediation of soil in diversifying rotation-fallow systems of garlic.</p>