Carboxymethyl chitosan (CMC) as a bio-based osteochondral inductive material was chemically immobilized on the surface of polycaprolactone (PCL) nanofibers to fabricate scaffolds for osteochondral tissue engineering applications. The chemical immobilization process included the aminolysis of ester bonds and bonding of the primary amines with glutaraldehyde as a coupling agent. The SEM and FTIR results confirmed the successfulness of the CMC immobilization. The fabricated scaffolds presented cell viabilities of > 82% and supported the attachment and proliferation of the human bone marrow mesenchymal stem cells (hBM-MSCs). The CMC-immobilized scaffolds concentration dependently induced the diverse osteochondral differentiation pathways for the hBM-MSCs without using any external differential agents. According to the Alcian Blue and Alizarin Red staining and immunocytochemistry results, scaffolds with a higher content of CMC presented more chondro-inductivity and less osteoinductivity. Thus, the CMC-immobilized scaffolds can be employed as great potential candidates for osteochondral tissue engineering applications.