Single-cell analysis is a valuable tool to dissect cellular heterogeneity in complex systems1. Yet, a comprehensive single-cell atlas has not been achieved for humans. We used single-cell mRNA sequencing to determine the cell-type composition of all major human organs and constructed a scheme for the human cell landscape (HCL). We revealed a single-cell hierarchy for many tissues that have not been well characterised. We established a ‘single-cell HCL analysis’ pipeline that helps to define human cell identity. Finally, we performed a single-cell comparative analysis of landscapes from both human and mouse to reveal the conserved genetic networks. We found that stem and progenitor cells exhibit strong transcriptomic stochasticity, while the differentiated cells are more distinct. Our study provides a valuable resource for human biology.