The important role of m6A RNA modification on β cell function has been established, yet how it regulates pancreas development and endocrine differentiation remains unknown. Here, we generated transgenic mice lacking RNA methyltransferase-like 3 (Mettl3) specifically in Pdx1+ pancreatic progenitor cells and found the mutant mice developed hyperglycemia and hypo-insulinemia at 2 weeks of age, with atrophic pancreas, reduced islet mass and abnormal increase in duct formation. At E15.5, Mettl3 deletion caused a significant loss of Ngn3+ endocrine progenitor cells, which was accompanied by increased Sox9+ duct precursor cells. We identified histone deacetylase 1(Hdac1) as the critical direct m6A target in bipotent progenitor, whose degeneration caused abnormal activation of Wnt/Notch signaling pathway and blocked endocrine differentiation. This transformation could be manipulated in embryonic pancreas culture in vitro through the regulation of the axis of Mettl3-Hdac1-Wnt/Notch signaling. Our finding that Mettl3 determines endocrine lineage through modulating Hdac1 activity during the transition of bipotent progenitor might help in the development of targeted endocrine cell protocols for diabetes treatment.