Light serves as the energy source as well as a signal for plant growth and development during their whole life cycle. Seedling de-etiolation is the most dramatic manifestation of light-regulated plant development processes, as massive reprogramming of the plant transcriptome occurs. Although there were organ-specific development and genome expression studies reported, there still lack a systematic analysis of cell type specific differentiation and the associated genome transcriptional regulation. Here, we obtained single-cell transcriptional atlases for etiolated, de-etiolating and light-grown Arabidopsis (Arabidopsis thaliana) whole seedlings. These atlases comprised 31,796 and 61,065 informative cells from shoot and root tissues, respectively, that were clustered and annotated as 48 different cell types. With the determination of comprehensive developmental trajectories, light modulation of cell fate differentiation during guard cell specialization and vasculature development have been demonstrated. Comparison of wild type and the pifs mutant indicates that PIFs involved in independent regulations in endodermis and stomatal lineage cells, by controlling cell type specific expression of target genes. Our results provide information concerning the light signaling networks at the cell-type resolution, improving our understanding of how light regulates plant development at the cell-type and genome-wide levels. The obtained information could serve as a valuable resource for comprehensively investigating molecular mechanism of cell development and differentiation in response to light.