Repairing articular cartilage by combining microfracture and various scaffolds has been extensively performed in in vivo animal models. We previously described a novel extracellular matrix (ECM) scaffold for cartilage tissue engineering. The aim of this study was to investigate the effect of a bone marrow-derived mesenchymal stem cells-derived ECM (BMSC-dECM) scaffold on the chondrogenic differentiation of marrow clots following microfracture in vitro. In this study, we manufactured the BMSC-dECM scaffold using a freeze-drying method. To obtain the marrow clots, a full-thickness cartilage defect was established and microholes were created in the trochlear groove of New Zealand white rabbits. The samples were divided and cultured in vitro for 1, 2, 4, and 8 weeks. The samples included a culture of the marrow clot alone (Group 1), a culture of the marrow clot with transforming growth factor-beta 3 (TGF-β3) (Group 2), a culture of the composite of the BMSC-dECM scaffold and the marrow clot alone (Group 3), and a culture of the composite with TGF-β3 (Group 4). A smooth and glossy surface was observed in Group 2 and Group 4 over time, but the surface for Group 4 was larger from week 1 onward. Compressive strength gradually increased in Groups 2 and 4, and greater increases were observed in Group 4 during the 8-week culture period. Enhanced cartilage-like matrix deposition of glycosaminoglycan (GAG) and type II collagen were confirmed by Safranin O and immunohistochemistry staining, respectively, in Groups 2 and 4. The GAG and collagen contents also gradually increased over time in Groups 2 and 4; the increase was greater in Group 4. In addition, real-time-polymerase chain reaction demonstrated that the expression of chondrogenic genes, such as COL2, ACAN, and SOX9, was gradually upregulated in Groups 2 and 4. However, greater increases in the expression of these cartilage-like genes were observed in Group 4 from week 4 onward. Our results suggest that the BMSC-dECM scaffold may favor the chondrogenesis of marrow clots following microfracture in vitro. In conclusion, these tissue engineering-like constructs could be potential candidates for cartilage repair.