AbstractThe underlying mechanisms that determine gene expression and chromatin accessibility in retinogenesis are poorly understood. Herein, single‐cell RNA sequencing and single‐cell assay for transposase‐accessible chromatin sequencing are performed on human embryonic eye samples obtained 9–26 weeks after conception to explore the heterogeneity of retinal progenitor cells (RPCs) and neurogenic RPCs. The differentiation trajectory from RPCs to 7 major types of retinal cells are verified. Subsequently, diverse lineage‐determining transcription factors are identified and their gene regulatory networks are refined at the transcriptomic and epigenomic levels. Treatment of retinospheres, with the inhibitor of RE1 silencing transcription factor, X5050, induces more neurogenesis with the regular arrangement, and a decrease in Müller glial cells. The signatures of major retinal cells and their correlation with pathogenic genes associated with multiple ocular diseases, including uveitis and age‐related macular degeneration are also described. A framework for the integrated exploration of single‐cell developmental dynamics of the human primary retina is provided.