Ginkgo biloba L. is considered one of the most ancient seed plants, with several primitive features of plant reproductive process. However, the phylogenetic position of Ginkgo and its relationship with other extant seed plants remain unclear. To gain a better understanding of these issues, we observed the embryological development of G. biloba using semi-thin sections and scanning electron microscopy. In late August, the zygote moved from the end of the micropylar to the middle of the archegonium, and mitosis resulted in many free nuclei distributed randomly in the archegonium. Afterwards, the cell wall was formed and the proembryo began to differentiate into the embryonal region and the underdeveloped presuspensor region. In early October, the embryo differentiated into two cotyledons, plumule, hypocotyl, radicle, and suspensor tissues. Subsequently, the two cotyledons grew rapidly, but the undeveloped suspensor began to degenerate and gradually disappear, indicating that the embryo had begun to mature. During early embryo development, the main supply of nutrients was carbohydrate in the cells of the jacket, tentpole, and surrounding endosperm, whereas endosperm provided nutrients during embryo maturation. Our results indicate that Ginkgo is extremely similar to cycads in terms of embryology but more similar to conifers in macromorphology and vegetative anatomy, suggesting that the Ginkgo lineage may have an intermediate phylogenetic position between cycads and conifers.