In the study of the pathogenesis of joint diseases, the most commonly targeted subjects are bone, cartilage and synovial tissue. At present, it is mainly to explore the possible pathogenesis and pathogenesis from the pathological changes of these tissues. So there are a lot of limitations and inaccuracies, such as ignoring the role of the heterogeneity of individual cells within the disease organization in the disease. Single-cell sequencing is a technique for sequencing genomes, transcriptomes, and epigenomes at a single cell level, enabling to obtain heterogeneous information from different cells and to sequence precious microsamples ，even to reflect the laws and essence of life in a deeper level. here we summary the basic methods of single-cell sequencing technology and its application in joint diseases.