Embryo-endosperm interaction strongly affects the developmental process of seeds and hence the formation of crop yield and quality. However, signals that orchestrate developmental processes of the two compartments are largely unknown. This study aims to provide an integrative landscape of rice seed development by organizing the information about embryo-endosperm interaction. Using a mutant with notched-belly grains, we devised a novel comparison method that can quantitatively evaluate the effect of embryo on the developmental process of endosperm, by comparing the upper and bottom endosperms of the mutant. Global comparison of mRNAs datasets in embryo and endosperm samples collected from 5 DAF (day after fertilization) through maturity uncovered a dragging effect of embryo on the developmental transition of the endosperm, extending the middle stage and delaying the late stage. Biochemical analysis revealed that signaling pathways of T6P-SnRK1, and GA or IAA may be involved in mediating this developmental transition. Integrating the information about embryo-endosperm bidirectional dialogue enables a new rice seed developmental staging system to be proposed. The results obtained should be valuable for elucidating the biological processes and signatures of grain formation, hence providing a valuable resource for modifying the molecular and physiological processes responsible for cereal grain yield and quality.