Abstract: Ion Torrent, as an innovative chip sequencing technology, has the advantages of simplicity, speediness and efficiency. It shows great ability in the field of life science research. The main steps include: preparation of the library, preparation of the ion sphere particles (ISPs) of the template-positive ion PGM^TM template, chip sequencing and data analysis. One of the key steps of the experiment is to prepare the ISPs of the template-positive ion PGM^TM template. In this study, flow cytometry is used to evaluate the quality control of enriched ISPs before the next step of the sequencing experiment, so as to reduce the cost of time and reagent caused by the unsuccessful preparation of ISPs, and improve the efficiency of sequencing.