Vibrio natriegens is a fast-growing gram-negative bacterium with a doubling time of less than 10 minutes. A slower growth mutant was obtained under SMG by continuously culturing long for two weeks. After obtained the genome conformation of the strain with chromatin conformation capture (Hi-C), we found that differentially expressed genes were located in those regions with chromosome structure variation and mainly related to the transcription of global regulatory factors and flagellin. Meanwhile, a significant portion of SNPs were found in the regions with higher interaction frequencies than the average of the whole genome. The microgravity may regulate the local gene expressions by sensing stress changes through global regulatory factors and by conformation changes in the region of genes involved in flagellin and adaptability, followed by altering some physiological characteristics and then affecting growth rate and metabolic capacity thereof.