The phenotypic responses of human bone marrow mesenchymal cells (hBMSCs) on different ratio of chitosan/polycaprolactone (PCL) blends were investigated in this study. The results showed that hBMSCs existed different morphology on chitosan/PCL blends due to the different adhesion characteristic of cell on neat PCL and neat chitosan. Interestingly, comparing to hBMSCs on neat PCL, hBMSCs aggregated to form spheroid and to express ascendant trend of transforming growth factor β1, collagen type II, collagen type X, and Sox9 mRNA on the chitosan/PCL blended substrates with the decrease of PCL content. To confirm chondrogenesis of hBMSCs with spheroid on test substrates, Alcian Blue and Safranin O staining were used to detect the cartilaginous extracellular matrix (ECM). It revealed hBMSCs with spheroid on neat chitosan and 10 wt % PCL did turn to chondrogenic differentiation and synthesize cartilaginous ECM. Therefore, these findings provided new insights into the role of chitosan/PCL blended material could mediate the endogenous gene expression of hBMSCs to alter the phenotypic behavior through mediating the cell shape.