Wnt/β-catenin signaling plays a critical role in colonic carcinogenesis. However, non-coding RNAs (ncRNAs) transcriptionally regulated by β-catenin are largely unknown. Herein, we found that lncRNA MIR100HG (lnc-MIR100HG) negatively correlated with target genes of β-catenin from The Cancer Genome Atlas colorectal carcinoma (CRC) database, which was verified in 48 paired CRC specimens. In addition, constitutive overexpression of β-catenin decreased primary and mature lnc-MIR100HG levels, while blockage of β-catenin activity with siRNA or inhibitors significantly increased their expression. DNA pull-down and chromatin immunoprecipitation revealed the binding of β-catenin/TCF4 to the MIR100HG promoter. Moreover, β-catenin forced expression reduced the enrichment of H3K27Ac, an active transcription marker, on the promoter, while β-catenin inhibition reversed this effect. Furthermore, HDAC6 was recruited to the MIR100HG promoter and downregulated H3K27Ac enrichment in a β-catenin-dependent manner. Besides, HDAC6 was upregulated and negatively correlated with lnc-MIR100HG in CRC specimens. Functional studies showed that lnc-MIR100HG overexpression induced cell cycle G0/G1 arrest and repressed cell proliferation via p57 upregulation in vitro and in vivo. Taken together, we found that ectopic β-catenin transcriptionally repressed lnc-MIR100HG expression through HDAC6-mediated histone modification in CRC. Lnc-MIR100HG regulates the cell cycle through p57. Implications: It provides a novel downstream mechanism highlighting β-catenin action during colon carcinogenesis and may shed light for further therapeutic approaches.