As a key area affected by secondary soil salinization in China, there is limited relevant research data on the formation mechanisms, as well as their influencing factors, in the Ningxia Autonomous Region. In this study, soil samples were collected at various soil depths in the Shizuishan area, Ningxia. A 16S rRNA-related PCR-DGGE technique was used to analyze bacterial diversity and dominant populations at different depths to explore the causes of salinization and its improvement measures from the perspective of soil ecology. Results from band similarity and UPGMA clustering indicated that the degree of bacterial diversity in the surface (D < 20 cm) and bottom (D > 80 cm) layers were similar and relatively high, whereas it was low in the middle layer (20 cm < D < 80 cm). The diversity indices analysis demonstrated that with increasing depth, the degree of richness and diversity tended to decline; whereas the degree of uniformity did not change considerably. Sequence comparison of five clones showed that the most predominant bacterial communities in this region were Proteobacteria and Bacteroidetes, whereas the remaining bands were not identified. The results of this study indicated that the degree of microbial diversity in saline-alkali soil in this area is very high, and the predominant bacterial flora is not the same. Generally, the bacterial diversity showed a linear relationship with depth, which is possibly related to the soil moisture content. However, more profound and in-depth data is needed to support this study. This study aimed to provide a theoretical reference for further in-depth study on secondary salinized soil formation mechanisms and their influencing factors.