Single-cell RNA sequencing (scRNA-seq) was recently adopted for exploring molecular programmes and lineage progression patterns of pathogenesis of important diseases. In this study, scRNA-seq was used to identify potential markers for chondrocytes in osteoarthritis (OA) and to explore the function of different types of chondrocytes in OA. Here we aimed to identify the biomarkers and differentiation of chondrocyte by Single-cell RNA seq analysis. GeneOntology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were used to identify the function of candidate marker genes in chondrocytes. Protein-protein interaction (PPI) network was constructed to find the hub genes in 3 types of chondrocyte respectively. We also used qRT-PCR to detect the expression level of the candidate marker genes in different types of chondrocyte. In this study, we characterized the single-cell expression profiling of 480 chondrocyte samples and found hypertrophic chondrocyte (HTC), homeostatic chondrocyte (HomC) and fibrocartilage chondrocyte (FC) respectively. The results of GO and KEGG analysis showed the candidate marker genes made specific function in these chondrocytes to regulate the development of OAs respectively. We further revealed the differential expression of top 10 marker genes in 3 types of chondrocyte. The marker genes of HTC and FC were mainly expressed in their cell subset respectively. The marker genes of HomC did not have obviously differential expression among different types of chondrocyte. Last, we predicted the key genes in each cell subset. CD44, JUN and FN1 were predicted tightly related to the proliferation and differentiation of chondrocytes in OAs and could be regarded as biomarkers to estimate the development of OA. Our results provide new insights into exploring the roles of different types of chondrocyte in OA. The biomarkers of chondrocyte were also valuable for estimating OA progression.