Plant and animal embryogenesis are distinct in several ways, such as unequal contributions of parents and differential levels of totipotency loss. However, the epigenomic processes regulating plant embryogenesis remain elusive. Here, we elucidate transcriptome trajectory and chromatin dynamics during embryogenesis of the most cultivated crop hexaploid wheat. Time-series analysis reveals stage-specific and proximal-distal distinct chromatin accessibility and epigenomic dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3 and H3K27ac for gene activation and H3K27me3 for gene repression differs from mouse or human, likely representing speices-specific epigenomic signatures. During early embryogenesis, remodeling of H3K27ac, H3K27me3, and chromatin accessibility establish a permissive environment increasing the accessibility of transcription factors to cis-elements that govern fate patterning afterward. Embryonic maturation is characterized by gaining H3K27me3 and losing chromatin accessibility, likely restricting totipotency while preventing extensive organogenesis. Finally, we identify epigenomic signatures correlate with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic basis of subgenome diversification in an allohexaploid genome. Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis.