Background: The iron acquisition ability of hypervirulent Klebsiella pneumoniae (hvKP) is an important part of its super virulence mechanism, increasing studies have proved that outer membrane vesicles (OMVs) are involved in the iron acquisition process of bacteria. Thus, we compared the difference in RNA expression in OMVs of hvKP in iron-rich and iron-deficient medium, and explore the possible mechanism of RNA in OMVs involved in hvKP iron acquisition. Results: The results of high-throughput sequencing showed that in iron-deficient medium, there were 239 up-regulated and 89 down-regulated mRNAs in OMVs of hvKP, of which 20 mRNAs related to iron transport was up-regulated, mainly including siderophore synthesis and receptor genes, ATP binding cassette transporter family and iron sulfur cluster. Only two of the differential ncRNAs that regulate these mRNAs are up-regulated, which are lncRNAs.Conclusion: We demonstrated that mRNA and lncRNA in OMVs were directly or indirectly involved in the iron acquisition mechanism of hvKP under iron deficiency environment, which enhanced the adaptive survival ability of hvKP. It provided a basis for further exploring the iron acquisition mechanism of OMVs involved in hvKP.