The aim of this study was to understand the effect of deep vertical rotary tillage on the diversity and structural distribution of a soil bacterial community in cultivated land, as well as the interactions between microbial ecological molecular network and species. In this study, the cultivated soil under different tillage methods in the Yellow River diversion irrigation area in Ningxia was selected as the research object, and two treatments were set up, namely, deep vertical rotary tillage (DVRT) and conventional tillage (CT). Then, Illumina MiSeq technology was used to analyze the molecular ecological network of soil bacterial community under different tillage methods in the Ningxia Yellow River irrigation area. The results showed that DVRT significantly increased the contents of total organic carbon (TOC), total nitrogen (TN), alkali-hydrolyzed nitrogen (AN), total phosphorus (TP), available phosphorus (AP), and total potassium (TK) in the 0-20 cm soil layer compared with those in the CT treatment. Compared with those in the CT treatment, DVRT significantly increased the contents of TOC, TN, TP, AP, TK, and available potassium (AK) in the 20-40 cm soil layer. DVRT treatment significantly increased water content (WC) by 8.13%-13.30% and decreased pH and electrical conductivity (EC) by 4.51%-5.85% and 12.5%-13.33%, respectively. In different growth stages and soil layers of maize, the Shannon and Ace indices were increased in the DVRT treatments. The dominant bacterial phyla were:Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteriota, and Gemmatimonadota. The results of bacterial community β diversity showed that DVRT and CT had significant differences in bacterial community structure. The redundancy analysis and Partial Mantel test results showed that pH, EC, and TP were the key environmental factors affecting the structural diversity of bacterial communities. Molecular ecological network analysis revealed that DVRT treatment microbial networks consisted of more functionally related microbial modules, and the topological roles of key microorganisms were different from those in the CT treatment. In conclusion, DVRT can enhance soil nutrients and WC in different soil layers, reduce pH and EC, improve soil bacterial community diversity and microbial network structure, and also enhance the potential ecosystem functions in cultivated soil.