Ischemic stroke is an acute cerebrovascular disease with high disability and mortality, is the most common cause of death in China. Despite years of research, there are still no biomarkers for stroke, and the molecular mechanisms remain largely unknown. In the past decade, single-cell sequencing technology, as a rapidly developing emerging technology, can conduct high-throughput sequencing of multiple omics including genome, transcriptome, epigenome and proteome at the level of a single cell, providing a new way to discover biomarkers and analyze pathological mechanisms. In this paper, the progress of single-cell multi-omics sequencing technology and its application in the discovery of biomarkers, pathological mechanisms and drug development of ischemic stroke are introduced in detail, in order to provide valuable reference for precision medicine of ischemic stroke.