Prenatal caffeine exposure (PCE) leads to intrauterine growth retardation and altered glucose homeostasis after birth, but the underlying mechanism remains unclear. This study aims to investigate the alteration of pancreatic development and insulin biosynthesis in the PCE female offspring and explore the intrauterine programming mechanism. Pregnant rats were orally treated with 120 mg/(kg∙day) of caffeine from gestational day (GD) 9 to 20. Results showed that fetal pancreatic β-cells in the PCE group exhibited reduced mass and impaired insulin synthesis function, as evidenced by decreased expression of developmental and functional genes and reduced pancreatic insulin content. At postnatal week (PW) 12, the PCE offspring exhibited glucose intolerance, diminished β-cell mass, and lower blood insulin levels. However, by PW28, glucose tolerance showed some improvement. Both in vivo and in vitro findings collectively indicated that excessive serum corticosterone (CORT) levels of the PCE fetuses may act through the activation of the pancreatic glucocorticoid receptor (GR) and recruitment of histone deacetylase 9 (HDAC9), leading to H3K9 deacetylation in promoter and downregulation of insulin-like growth factor 1 (IGF1), thereby inhibiting pancreatic islet morphogenesis and insulin synthesis in fetal rats. Furthermore, the PCE offspring after birth exhibited decreased blood CORT levels, increased H3K9 acetylation in promoter and upregulated gene expression of the pancreatic IGF1 promoter region, accompanied by elevated insulin biosynthesis. However, when exposed to chronic stress, the above changes were totally reversed. Conclusively, "glucocorticoid-insulin like growth factor 1 (GC-IGF1) axis" programming may be involved in pancreatic β-cell dysplasia and dysfunction in the PCE female offspring.