Klf6 is a member of the Krüppel-like factor family, which is a group of zinc finger transcription factors involved in differentiation and development. In general, Klf6 gene plays an important role in growth-related signal transduction pathways, cell proliferation, apoptosis, and angiogenesis. Recently, the Klf6 gene is considered as one of tumor suppressor genes in several kinds of tumours, but there is also a conflict of experimental data. In this study, we investigated the influence of Klf6-related super-enhancer (SE) on tumor cell growth in human hepatoma (HepG2) cells. As a result, SE-deleted clones were obtained via the CRISPR/Cas9-mediated gene-editing technique. Moreover, it was found that some crucial properties associated with malignancy in those clones were equally affected by the disruption of Klf6-related super-enhancer: proliferation, migration, clonogenic potential and drug resistance. These results contribute to the deeper understanding on the potential roles of the Klf6 related super enhancer in human hepatoma (HepG2) cells.