The invention discloses a bacterial HI-C genome and plasmid conformation capturing method. The method comprises the following capturing steps: bacterial culture, cross-linking reaction, sample integrity verification, bacterial lysis, chromatin digestion, biotin filling, ligation reaction, reverse cross-linking, library extraction, biotin removal, phenol chloroform DNA extraction and second generation library establishment. According to the method, DNA and protein are crosslinked together through formaldehyde treatment so as to fix the conformation of the DNA, enzyme digestion, biotin introduction, enzyme linkage and extraction are carried out, then library construction and high-throughput sequencing are carried out on treated nucleic acid, and finally, interaction information between bacterial chromatin fragments and between bacterial chromatin fragments and plasmids can be revealed by analyzing sequencing data. The method can be applied to genome assembly, gene expression regulation research and the like.