In this study, we provided evidence for ABCG2 as a drug-resistant gene up-regulated in chemo-insensitive cCSCs and CRC tissues through RNA-seq analysis and high-throughput screening and elucidated TOX3 as a pivotal regulatory factor to facilitate cCSCs self-renewal and drug resistance, including chemotherapy and targeted therapy, in vivo and ex vivo, by activating ABCG2 transcription. This evidence concerns the gene TOX3 and colorectal carcinoma.