Bacteria in desert soil have unique phylogeny and important ecological functions, and their responses to changes in precipitation need further attention. However, relevant studies have mainly focused on the surface soil, and studies on the responses of bacteria at different soil depths to variations in precipitation are rare. Thus, we used 16S rDNA high-throughput sequencing to investigate the changes in soil bacterial distribution along a mean annual precipitation gradient (50–150 mm) in the Alxa Desert, China, and compared the variation characteristics in the surface soil layer (0–10 cm) and subsurface soil layer (10–20 cm). Results showed that soil bacterial communities significantly changed along the precipitation gradient in both soil layers. However, the subsurface soil layer could support bacterial communities with higher diversity and closer internal relationships but more internal competition than the surface soil layer. Additionally, compared with the surface soil layer, variations in diversity and co-occurrence patterns in the subsurface soil layer were more in line with the changes in the mean annual precipitation, while bacterial community structure was less variable in the subsurface soil layer. Compared with the mean annual precipitation, soil moisture had little influence on the structure and diversity of soil bacterial community but had a high correlation with intercommunity connectivity. Therefore, soil moisture might play a complex role in mediating environmental conditions and soil bacterial community characteristics. Due to the different responses of surface and subsurface soil bacteria to the changes in precipitation, it is necessary to distinguish different soil layers when predicting the trends in desert soil bacterial conditions associated with precipitation, and prediction of subsurface soil bacteria may be more accurate.