Knowledge detailing human pre-gastrulation embryonic development including spatial self-organization and cell type ontogeny remains limited by available twodimensional technological platforms that do not recapitulate the in vivo condition. Here, we report a three-dimensional (3D) blastocyst-culture system, which enables human blastocyst development through primitive streak anlage (PSA) formation. These 3D-embryos mimic in vivo developmental landmarks and 3D-architectures, including embryonic disc, amnion, basement membrane, primary and primate unique secondary yolk sac, anterior-posterior polarity formation and PSA. Using single cell transcriptome profiling, we delineate ontology and regulatory networks underlying epiblast, hypoblast and trophoblast segregation. Compared to epiblast, the grown amniotic epithelium shows unique and characteristic phenotypes. After implantation, specific pathways and transcription factors trigger differentiation of cytotrophoblasts, extravillous cytotrophoblasts and syncytiotrophoblasts. Epiblast undergoes pluripotency transition upon implantation and maintains its transcriptome until PSA generation as coordinated by different pluripotent factors. Using our 3D-culture approach, our findings elucidate the molecular and morphogenetic developmental landscape during early human embryogenesis.