The invention discloses an organic mass spectrum flow cytometry technology which comprises the following steps: preparation of a protein labeled flow cytometry probe and a cell labeling method, construction of an organic mass spectrum flow cytometry device, mass spectrum flow cytometry detection of a cell suspension sample, and extraction and analysis of protein labels and metabolite information in a single cell mass spectrum. The technology is high in universality, the device is simple, and rapid, efficient, high-throughput and high-sensitivity sample analysis can be achieved. The flow mass spectrometry probe marks a large number of organic tags on target proteins, so that the detection sensitivity reaches the single cell level, qualitative and quantitative analysis of multiple target proteins and a large number of metabolites at the single cell level can be realized, and a large number of single cell level information is obtained. The technology has wide application prospects in the fields of cell identification, cell typing, research on characteristic difference substances in cells, tumor diagnosis, systematic biology research and the like.