Near-surface O3 has negative effects on plant productivity; however there were few studies on the effects of O3 pollution on the belowground part of the ecosystem. The effect of O3 stress on the belowground parts of poplar is unclear. We investigated the effects of O3 pollution on poplar rhizosphere soil in open-top chambers (OTC). Two kinds of plants with different O3 sensitivity were selected, i.e., high-sensitive poplar clone 546 and low-sensitive poplar clone 107. The control group and high-concentration O3 group were set up: charcoal-filtered air, CF; unfiltered air + 60 ppb O3, NF. Poplar rhizosphere soil was taken after 96 days (15 June to 17 September 2020) of cultivation in OTCs. O3 stress decreased the amplicon sequence variations (ASVs) of microorganisms in poplar 107 and poplar 546 rhizosphere soil, with no significant interspecific difference. The effect of O3 fumigation on the fungal community was greater than that on the bacterial community. The correlation between the bacterial community and rhizosphere soil physicochemical indices was closer than that of the fungal community. Some fungi, such as Clitopilus hobsonii, Mortierella sp., and Minimedusa, might help poplar resist the O3 stress. O3 stress had direct impacts on the pH, nutrients, and enzyme activities of rhizosphere soil, while it had indirect negative impacts on microbial community composition by nutrients. There was no difference in sensitivity between rhizosphere soil response to O3 stress of poplar clone 107 and clone 546, which might take a longer accumulation time to show the effect. This study provides a certain basis for accurately evaluating the ecological effects of O3 pollution.