CO2-EOR (enhanced oil recovery) has been proposed as a viable option for flooding oil and reducing anthropogenic CO2 contribution to the atmospheric pool. However, the potential risk of CO2 leakage from the process poses a threat to the ecological system. High-throughput sequencing was used to investigate the effects of CO2 emission on the composition and structure of soil bacterial communities. The diversity of bacterial communities notably decreased with increasing CO2 flux. The composition of bacterial communities varied along the CO2 flux, with increasing CO2 flux accompanied by increases in the relative abundance of Bacteroidetes and Firmicutes phyla, but decreases in the relative abundance of Acidobacteria and Chloroflexi phyla. Within the Firmicutes phylum, the genus Lactobacillus increased sharply when the CO2 flux was at its highest point. Alpha and beta diversity analysis revealed that differences in bacterial communities were best explained by CO2 flux. The redundancy analysis (RDA) revealed that differences in bacterial communities were best explained by soil pH values which related to CO2 flux. These results could be useful for evaluating the risk of potential CO2 leakages on the ecosystems associated with CO2-EOR processes.