• Relative abundances of microbial communities were most related to aggregate proportions in clay-layer soils.
• Aggregate content with<0.053 mm in clay-layer soil significantly influence the diversity of soil microbial community.
• Complexity of microbial interactions raised along increasing precipitation across sampling sites.
• Competition for substrates induced niche differentiation in deeper soils.
Soil microorganisms play a key role in the function of soil ecosystem, yet our knowledge about how microbial communities respond to the typically sandy soil environmental properties along the soil profile is still insufficient. We investigated the soil microbial community patterns from top (0 – 20 cm) to clay-layer (>80 cm) of the typical sandy soils in three regions in China with different levels of precipitation, including Lishu County in Jilin Province (LS), Langfang City in Hebei Province (LF) and Zhengzhou City in Henan Province (ZZ). Our findings showed that small-size aggregates (<0.5 mm) rather than large ones (>= 0.5 mm) dominated the soil profile. The relative abundances of Actinobacteria, Crenarchaeota and Firmicutes were highly related to aggregate proportions of the deep clay-layer soil. The network analysis revealed the distinct community patterns among modules, evidencing niche differentiation along the soil profile. The keystone species OTU_11292 was observed having migrated clearly into the other module of the clay-layer soil. Different roles of the OTU_30 (belonging to Gemmatimonadetes) in soil processes might partly explain the different microbial distribution between top- and clay-layer soils. These findings provided new insights into the candidate mechanisms of microbial diversity maintenance and community patterning of sandy soils, which were necessary for better understanding of ecological rules guiding long-term agricultural practice.