Abstract The cellular composition and underlying spatiotemporal transformation processes of subchondral bone in osteoarthritis (OA) remain unknown. Herein, various cell subsets from tibial plateau of OA patients are identified, and the mechanism of subchondral microstructure alteration is elaborated using single-cell RNA sequencing technique. We identified two novel endothelial cell (EC) populations characterized by either exosome synthesis and inflammation response, or vascular function and angiogenesis. Three osteoblast (OB) subtypes are introduced, separately related to vascularization, matrix manufacturing and matrix mineralization. The distinct roles and functions of these novel phenotypes in OA development are further discussed, as well as interaction network between these subpopulations. The variation tendency of each population is testified in a DMM mouse model. The identification of cell types demonstrates a novel taxonomy and mechanism for ECs and OBs inside subchondral bone area, provides new insights into the physiological and pathological behaviors of subchondral bone in OA pathogenesis.