Small ubiquitin-related modifier protein (SUMO) modification is a kind of widespread form of post-translational modification. It exists in multiple physiological and pathological processes, and is involved in a number of signal transduction pathways. Sumoylation is one of the important regulating mechanism in the cellular response to stress, and a growing body of research suggests that the SUMO play an important role in the process of embryonic development and organogenesis in mammals. Sumoylation plays an important role in the formation and development of organs in fetal development. The components of the sumoylation pathway (UBC9, SUMO1-3, PIAS, SENP1-7) play important roles in the coordination of the dialogue between the blastocyst and the uterus, the development of the heart, and craniofacial development. When these developmental dysfunctions occur, they can lead to preimplantation defects, developmental defects, and fetal death. In this review, we will focus on recent advances in this field, summarizing the important roles in early embryonic development and organogenesis of SUMO, UBC9, PIAS, and SENPs, which have been linked to the SUMO pathway, and the consequences of aberrant SUMOylation, to provide a reference for future research.