Cell metabolism plays a crucial role in regulating the pluripotency of human embryonic stem cells (hESCs). Chlorogenic acid (CGA), an essential dietary polyphenol, exhibits diverse pharmacological effects on metabolism regulation. This study examines the effects of CGA on cell metabolism in hESCs using the H9 model. At a concentration of 100 µg/ml, CGA showed low toxicity and had no impact on the viability of H9 cells. Furthermore, it promotes NANOG expression. Importantly, CGA enhances Fatty acid β-oxidation (FAO), thus promoting the proliferation and lipid synthesis of H9 cells. Mechanistically, CGA-induced FAO generates acetyl-CoA, which enhances de novo lipid synthesis and hyperacetylates H3K27 at the promoter regions of associated genes, thereby enhancing their expression. This study highlights the potential beneficial effects of CGA on cell proliferation and provides opportunities for optimizing the in vitro culture of hESCs.