The chromatin accessibility and 3D high-order structure play an important role in gene expression and regulation, and are involved in numerous cellular processes such as differentiation, development and tumorigenesis. It is currently one of the hottest research fields in epigenetics. The animal embryonic development initiates from the terminally differentiated mature eggs, which are fertilized by sperms to establish totipotent zygotes. During this complex process, the epigenome encompassing chromatin accessibility and high-order structures changes dramatically, undergoes inheritance, reprogramming and re-establishment, so that the zygote could eventually develop into a new multicellular and multi-tissue organism. In this review, we summarize the research methods and technology for chromatin accessibility and 3D high-order structures, the dynamics of chromatin structures during the animal embryonic development and how to regulate early embryogenesis, the relationship between chromatin structure and other epigenetic information such as methylation and histone modification. We hope that this review may shed light on the research of epigenome regulating embryo development.