The repair of osteochondral defects remains challenging, given the complexity of native osteochondral tissue and the limited self-repair capacity of cartilage. Osteochondral tissue engineering is a promising strategy. Here, we fabricated a biomimetic osteochondral scaffold using silk fibroin and hydroxyapatite, including a calcified cartilage layer (CCL). We studied the role played by the CCL in terms of cell viability in vivo. We established osteochondral defects in rabbit knees to investigate the effects of CCL-containing scaffolds with or without adipose tissue-derived stem cells (ADSCs). We evaluated osteochondral tissue regeneration by calculating gross observational scores, via histological and immunohistochemical assessments, by performing quantitative biochemical and biomechanical analyses of new osteochondral tissue, and via microcomputed tomography of new bone at 4, 8, and 12 weeks after surgery. In terms of surface roughness and integrity, the CCL + ADSCs group was better than the CCL and the non-CCL + ADSCs groups at all time points tested; the glycosaminoglycan and collagen type II levels of the CCL + ADSCs group were highest, reflecting the important role played by the CCL in cartilage tissue repair. Subchondral bone smoothness was better in the CCL + ADSCs group than in the non-CCL + ADSCs and CCL groups. The CCL promoted smooth subchondral bone regeneration but did not obviously affect bone strength or quality. In conclusion, a biomimetic osteochondral scaffold with a CCL, combined with autologous ADSCs, satisfactorily regenerated a rabbit osteochondral defect. The CCL enhances cartilage and subchondral bone regeneration.