Soil bacterial diversity and community composition are crucial for soil health and plant growth, and their dynamics in response to agronomic practices are poorly understood. The aim of this study was to investigate the response of soil bacterial community structure to the changes of sowing methods, soil depth and distance to roots in a winter wheat-summer maize crop rotation system on the Loess Plateau in china (35°17′38′′N, 111°40′24′′E). The experiment was laid out as completely randomized block design with three replications. Sowing methods trialed were: traditional sowing (TS), film-mulched ridge and furrow sowing (FMR&F), wide ridge and narrow furrow sowing (WR&NF) and unplanted control (CK). The result showed that the WR&NF sowing method treatment significantly decreased soil bacterial diversity (Chao 1 and Shannon indices) compared to the TS and FMR&F treatment, but increased abundance of beneficial bacteria such as genera Bacillus and Pseudomonas compared to the TS treatment. These genera showed a stronger correlation with soil properties and contributed to the soil nutrient cycling and crop productivity. Bacillus, Pseudomonas, Nevskia, and Lactococcus were the keystone genera in this winter wheat-summer maize rotation system on the Loess Plateau. Strong correlations between changes in soil properties and soil bacterial diversity and abundance were identified. In summary, we suggest that the WR&NF treatment, as a no-mulching film and no-deep tillage sowing method, would be the most suitable sowing technique in the winter wheat-summer maize rotation on Loess soil.