Clostridium acetobutylicum is an important strain for bio-butanol formation. In recent years, gene-editing technology is widely used for developing the hyper-butanol-production strains. In this study, three genes (cac1251, cac2118 and cac2125) encoding cell division proteins (RodA, DivIVA and DivIB) in C. acetobutylicum were knocked out. The cac2118-knockout strain had changed its cell morphology to spherical-shape during the solventogenesis, and obtained a higher butanol yield of 0.19 g/g, increasing by 5.5%, compared with the wild type strain. The glucose utilization and butanol production of cac1251-knockout strain decreased by 33.9% and 56.3%, compared the with wild type strain, reaching to 47.3 g/L and 5.6 g/L. The cac1251-knockout strain and cac2125-knockout strain exhibited poor cell growth with cell optical density decreased by 40.4% and 38.3%, respectively, compared with that of the wild type strain. The results indicate that cell division protein DivIVA made the differences in the regulation of cell morphology and size. Cell division proteins RodA and DivIB played significant roles in the regulation of cell division, and affected cell growth, as well as solventogenesis metabolism.