Abstract: The survival of multicellular organisms depends on the functional division of different types of cells. Although specific cell types share the same genome, they have unique developmental programs, as well as different abilities to play their role during development and respond to environmental variation. Thus, a key challenge in biology is to understand how genes are expressed in the right cells at the right time and at the right level. Recently, many novel tools have been developed for single-cell-omics research using cell-type-specific methods. These innovations enable us to understand the mechanisms of gene regulation in single cells and their adaptation to environmental changes with unprecedented resolution. The isolation of single-cell samples has long been a bottleneck to relevant study; however, there are some useful techniques available. In this paper, we discuss techniques for sample labeling, isolation and collection of single cells, -omics data analysis and validation for single-cell analysis, and their application for plant research.