Hypoxia-inducible factor 1α (HIF-1α) plays a key role in mediating cancer cell malignant characteristics. Recent studies have shown that the histone demethylase JMJD2B is a target of HIF-1α, suggesting that histone methylation may be involved in tumor malignancy during hypoxia. However, little is known about the tumorigenic role of JMJD2B and its association with hypoxia in colorectal cancer (CRC). Furthermore, the downstream target genes and the mechanisms by which JMJD2B regulates its target genes in CRC during hypoxia remain to be clarified. Our results demonstrated that JMJD2B was induced under hypoxia in an HIF-1α-dependent manner in CRC cells. JMJD2B played an important role in CRC cell proliferation, apoptosis, cell cycle arrest and invasion, which could be modulated through upregulation of a subset of hypoxia-inducible genes expression by decreasing trimethylation of histone H3 lysine 9 on their promoters. We also showed that JMJD2B was overexpressed in CRC tissues and positively correlated with expression of the hypoxic marker carbonic anhydrase 9 (CA9), deeper depth of invasion and advanced clinical stages. Therefore, our findings suggest that JMJD2B may serve as a potential therapeutic cancer target.