Nrf1 and Nrf2, as two principal CNC-bZIP transcription factors, regulate similar but different targets involved in a variety of biological functions for maintaining cell homeostasis and organ integrity. Of note, the unique topobiological behavior of Nrf1 makes its functions more complicated than Nrf2, because it is allowed for alternatively transcribing and selectively splicing to yield multiple isoforms (e.g., TCF11, Nrf1α). Here, to gain a better understanding of their similarities and differences in distinct regulatory profiles, four distinct cell models for stably expressing TCF11, TCF11ΔN, Nrf1α or Nrf2 have been established by an Flp-In™ T-REx™-293 system and identified by transcriptomic sequencing. Further analysis revealed that Nrf1α and TCF11 have similar yet different regulatory profiles, though both contribute basically to positive regulation of their co-targets, which are disparate from those regulated by Nrf2. Such disparity in gene regulation by Nrf1 and Nrf2 was also corroborated by scrutinizing comprehensive functional annotation of their specific and/or common target genes. Conversely, the mutant TCF11ΔN, resulting from a deletion of the N-terminal amino acids 2-156 from TCF11, resembles Nrf2 with largely consistent structure and function. Interestingly, our further experimental evidence demonstrates that TCF11 acts as a potent tumour-repressor relative to Nrf1α, albeit both isoforms possess a congruous capability to prevent tumour growth and upregulate those genes critical for improving the survival of patients with hepatocellular carcinoma.