Watermelons grown in sandy soil are rich in trace elements, particularly selenium, and are therefore also known as selenium-rich sand watermelons. However, continuous watermelon cultivation in the same sandy field decreases soil fertility and degrades the ecosystem, ultimately resulting in low-quality watermelons. Introducing different crops into the crop pattern could alleviate the problems posed by continuous cropping. A field experiment was conducted to explore the effects of different crop patterns on soil microbial communities and soil properties via standard techniques. The results showed that 14,905 bacterial and 2150 fungal operational taxonomic units were obtained and assigned to eight bacterial and five fungal phyla, respectively. Soil bacterial communities primarily comprised Proteobacteria, Planctomycetes, Actinobacteria, and Acidobacteria, and the soil fungal community was dominated by Ascomycota, Chytridiomycota, and Basidiomycota. Different crop patterns had a significant effect on the Chao and ACE indexes of fungal communities in the soil. The rotation of six years of watermelon and one year of wheat had the highest richness indexes of all the rotations. Different crop patterns had significant effects on soil properties, such as organic matter (OM), total nitrogen (TN), total potassium (TK), available phosphorus (AP), available K, nitrate nitrogen (NN), and pH. The soil OM, TN, NN, and pH of six years of watermelon and one year of wheat cultivation were significantly higher than those of the other three crop patterns. In addition, the soil TK and AP of the continuous watermelon planting treatment were significantly higher than those of the other three crop patterns. Redundancy analysis results revealed many complex relationships between soil properties and soil bacterial or fungal communities. Employing different crop patterns plays an important role in the effective regulation of soil microbial diversity and properties.