Enhancer of zeste homolog 2 (EZH2), a catalytic component of polycomb repressive complex 2 (PRC2), epigenetically regulates chromatin structure and gene expression through trimethylation at histone H3K27 and recruitment of DNA methyltransferases for gene silencing. Despite extensive studies of the role of EZH2 in cancer progression and malignancy, increasing evidences suggest that EZH2 plays a critical role in stem cells renewal, maintenance, and differentiation into specific cell lineages. Here, we reviewed the update information regarding how EZH2 contributes to stem cell maintenance and cell lineage determination (including gonadogenesis, neurogenesis, myogenesis, osteogenesis, hematopoiesis, lymphopoiesis, adipogenesis, epidermal differentiation and hepatogenesis), and the regulation of EZH2 by phosphorylation and different signaling pathways.