Cell-to-cell variation and heterogeneity are fundamental and intrinsic characteristics of stem cell populations, but these differences are masked when bulk cells are used for traditional omic analysis. Technologies such as single-cell genome, epigenome and transcriptome sequencing have been developing rapidly in recent years. Single cell sequencing technologies serve as powerful tools to comprehensively dissect cellular heterogeneity and to identify distinct phenotypic cell types. The application of these methods to different types of stem cells, including pluripotent stem cells and tissue-specific stem cells, has led to exciting new findings in the stem cell field. This paper reviews the recent progress as well as future perspectives in the methodology and application of single-cell omic sequencing technologies.