The importance of early embryonic development in ensuring human health has long been recognized. Insights into the mechanisms of human early embryonic development can potentially contribute towards improving public health and reversing population aging, and promoting economic and social development. However, our knowledge of regulation networks that underpin human early embryonic development is far from complete due to technological and ethical constrains. Recently, incredible progress in scientific research on in vitro culture of mammalian embryos and embryoid technology represents a great opportunity in disclosing the mystery of human early embryonic development but also presents the toughest ethical challenges. Here we systematically review the major progress of research on early mammalian (rodent and primate) embryonic development, discuss the ethical debates about human embryo research, and lay out the future direction for the study of the early embryonic development regulation for both basic research and clinical application.