Icariside II, a flavonol glycoside, one of the major components of Traditional Chinese Medicine Herba epimedii. In the present study, we found that Icariside II suppressed the proliferation of CRC by inducing cell cycle arrest and apoptosis in vitro and inhibited tumor growth in vivo. The further mechanism investigation showed that Icariside II suppressed the expression of β-catenin and led to the functional inactivation of Wnt/β-catenin signaling. Circβ-catenin was considered as a promising candidate for mediating the tumorigenesis and the activation of Wnt/β-catenin signaling in CRC cells. Furthermore, Icariside II has been proven to suppress the biogenesis of circβ-catenin via epigenetically targeting DNA methyltransferases (DNMTs) to decrease global DNA methylation levels in CRC cells. Taken together, our results indicated that Icariside II suppressed tumorigenesis by epigenetically silencing the activation of circβ-catenin-Wnt/β-catenin axis in colorectal cancer. More importantly, the information gained from this study suggest that Icariside II may have great potential to be developed as a therapeutic drug for CRC patients.