Oil pollution poses a significant threat to soil properties and microorganisms in resource-enriched areas. However, the understanding of how the characteristics of the abundant and rare bacterial subcommunities change, as well as their driving factors, in the natural restoration process of petroleum-contaminated soil remains unclear. In this study, we compared the diversity, species richness, composition, co-occurrence network and their drivers of rare and abundant bacterial subcommunities in different natural restoration years (1, 7, 15, 20 years) at oil well sites in the Loess Plateau of China. Our results indicated that the diversity and relative abundance of soil bacterial abundant subcommunities were significantly higher than those of rare bacterial subcommunities at each restoration stage. This suggests that the abundant subcommunities dominated the changes of microbial community structure. The diversity of bacterial rare subcommunities continued to increase significantly with increasing restoration years, while the diversity of bacterial abundant subcommunities did not change significantly after 7 years of restoration. There are significant differences in the community structure between abundant and rare bacterial subcommunities. Abundant subcommunities had a wider niche and a more complex network structure, while rare subcommunities exhibited higher network modularity. Both the community characteristics of abundant and rare bacterial subcommunities were significantly affected by vegetation community indicators. Additionally, the abundant subcommunities were also affected by soil nitrogen-related indicators, while the rare subcommunities were jointly affected by soil nitrogen and phosphorus-related indicators. Overall, our research highlights the notable disparities in the characteristics and driving factors of soil abundant and rare bacterial subcommunities during the natural restoration process of oil well sites. Future assessments of soil restoration in petroleum development areas should pay attention to the differentiated responses of different microbial groups.