Single-cell RNA-seq provides information on the differences in gene expression, making it possible to study the cells and the mechanism of their interactions at the single-cell level. In recent years, single-cell transcriptome technology has experienced the development at the principle of cDNA amplification from homopolymer tailing-based, in vitro reverse transcription to template-switch, and greatly improved the sensitivity. At the same time, cell isolation is promoted from 96/384 well plates, droplets to nano-pores, which greatly reduced the experimental cost while increasing the throughput. The single-cell RNA-seq, with its advantages in cell heterogeneity and cell classification, has promoted the construction of cell atlas from developmental biology to normal tissue and pathological cell biology. This paper reviews the recent progress of single-cell RNA-seq and its application in human cell atlas.