ABSTRACT Ionic liquids (ILs) are widely used in various fields due to their excellent properties. Despite their utility, there is limited knowledge regarding the phytotoxic properties of ILs and the mechanisms by which plants develop resistance to them. This is particularly true when considering the role of nitric oxide (NO) in response to ILs stress. Herein, we investigated the mechanism by which endogenous NO reduces the ILs’ phytotoxicity in Arabidopsis from the perspective of rhizosphere microorganisms. We investigated the impact of 1,3-dibutyl imidazole bromide (DIB) on microbial diversity and community in the rhizosphere of Arabidopsis lines with varying endogenous NO levels, using a high throughput sequencing method. DIB did not affect microbial taxon numbers, richness, or evenness; however, it did alter microbial beta diversity and community structure in the rhizosphere of Arabidopsis. Elevated endogenous NO increased fungal richness and evenness, shifted DIB’s impact on microbial community structure, and enriched more resistant species and toxin-decomposing species. These findings suggest a potential mechanism for plants to resist IL stress. Our study not only elucidates the toxicological mechanisms of ILs but also reveals the involvement of NO in plant responses to IL stress, providing valuable insights for future environmental risk assessments and mitigation strategies.