Abstract: Flow cytometry is a biological technique for counting and sorting out tiny particles suspended in fluid based on flow cytometer through the detection of scattering or coupled fluorescence signals to obtain a series of important biophysical and biochemical related characteristics of suspended particles (usually cells, bacteria and other tiny particles) in a quick, accurate, objective and high-throughput way, and to automatically analyze and sort out specific populations according to the pre-selected parameter range of cells, bacteria and other tiny particles. Flow cytometry is widely used in many scientific fields, especially biotechnology and medicine. Although the application of flow cytometry in agricultural research started relatively late, great progress has been made. With the continuous improvement of the performance of flow cytometer, the continuous development and improvement of labeling methods and detection technologies, the application prospect of flow cytometry will become wider, and it will also play an increasingly important role in the agricultural field. In this review, it introduces the working principle and functional classification of flow cytometer, discusses the application and research progress of flow cytometry in agricultural fields such as crop genome and protoplast analysis, stress resistance research, animal immunity and trace element analysis, sperm quality and sex control, toxin toxicity analysis, pathogenic bacteria and virus analysis, and then looks forward to the development prospect of this research field, providing a new direction for the potential application of flow cytometry in agricultural fields.