To reveal the structure characteristics of microbial communities in regional groundwater at different depths and the interaction between microbial communities and groundwater environment, Liuli River district located in the southwestern Beijing was selected to collect different deep groundwater samples for the hydrochemical analysis and the high-throughput sequencing of the V4-V5region of microbial 16S rRNA. The results of hydrochemistry showed that the concentration of eight main ions decreased with the increase of depth in groundwater, especially Cl^-, SO₄^2- and NO₃^- varied obviously. In industrial area, the highest concentrations of NO₃^- and SO₄^2- were up to 155.30mg/L and 321.00mg/L, respectively, where shallow groundwater was contaminated with NO₃^- and SO₄^2-. Microbial analysis showed that the diversity of microbial community was strongly affected by groundwater depth, and microbial abundance increased with the increase of groundwater depth. Proteobacteria(26.2%~95.2%)was the dominant phylum and Pseudomonas (1.5%~32.2%)was the dominant genus. The microbial community at different depths of groundwater was significantly different. The number of the specific genera of shallow, middle and deep aquifer were 74, 60 and 54, respectively. NO₃^-, SO₄^2-and depth were the main factors affecting the microbial community. In addition, the concentrations of NO₃^- and SO₄^2- were closely related to depth. Groundwater depth was an important control factor to microbial community structure.