Abstract: Desorption electrospray ionization mass spectrometry (DESI-MS) is a newly emerging in-situ ionization mass spectrometry analysis technology. The ionization process occurs in an open ambient environment at atmospheric pressure, and has the characteristics of simple sample pretreatment, quick and sensitive analysis, and is widely used in biomedicine, pharmaceutical analysis, food safety, environmental monitoring, and material characterization. Natural medicines, such as Chinese herbal medicines, contain a variety of chemical components. Extraction, separation, identification, and in vitro and in vivo efficacy evaluation of natural medicines, especially research on active ingredients with significant efficacy, have received long-term attention. The development of DESI-MS technology provides many new opportunities for direct and rapid analysis of active ingredients in natural medicines. This article briefly introduces the principles, characteristics, influencing factors, and technical progress of DESI-MS technology, and systematically summarizes progress in the research and application of this technology to natural medicines such as Chinese herbal medicines and other plant samples with pharmacological activity. The future application prospects in this field are further presented.