Epigenetic programming and reprogramming, by means of DNA methylation and histone modifications etc., control the mammalian development to a large extent. They are also artificially altered for cell fate conversion and regeneration. Though epigenetic modifications change with slow dynamics during somatic cell lineage differentiation, they undergo a genome-wide dramatic change with extensive DNA de-methylation and histone modification during two specific time windows, the early embryogenesis and the Primordial Germ Cell (PGC) development stage. Here we reviewed these global epigenetic reprogramming occurred during normal development, mainly focusing on DNA methylation, histone modification and X-chromosome inactivation. Epigenetic reprogramming participates in many key biological processes such as genomic imprinting, X-chromosome inactivation, gene expression regulation and tumorigenesis and genome stability. Understanding the mechanisms of epigenetic reprogramming during the early embryogenesis and PGC formation would facilitate our knowledge of the developmental process and disease progress.