Background: One of the main problems associated with the development of osteochondral reparative materials is that the accurate imitation of the structure of the natural osteochondral tissue and fabrication of a suitable scaffold material for osteochondral repair are difficult. The long-term outcomes of single-or bilayered scaffolds are often unsatisfactory because of the absence of a progressive osteochondral structure. Therefore, only scaffolds with gradient pore sizes are suitable for osteochondral repair to achieve better proliferation and differentiation of the stem cells into osteochondral tissues to complete the repair of defects. Methods: A silk fibroin (SF) solution, chitosan (CS) solution, and nano-hydroxyapatite (nHA) suspension were mixed at the same weight fraction to obtain osteochondral scaffolds with gradient pore diameters by centrifugation, freeze-drying, and chemical cross-linking. Results: The scaffolds prepared in this study are confirmed to have a progressive structure starting from the cartilage layer to bone layer, similar to that of the normal osteochondral tissues. The prepared scaffolds are cylindrical in shape and have high internal porosity. The structure consists of regular and highly interconnected pores with a progressively increasing pore distribution as well as a progressively changing pore diameter. The scaffold strongly absorbs water, and has a suitable degradation rate, sufficient space for cell growth and proliferation, and good resistance to compression. Thus, the scaffold can provide sufficient nutrients and space for cell growth, proliferation, and migration. Further, bone marrow mesenchymal stem cells seeded onto the scaffold closely attach to the scaffold and stably grow and proliferate, indicating that the scaffold has good biocompatibility with no cytotoxicity. Conclusion: In brief, the physical properties and biocompatibility of our scaffolds fully comply with the requirements of scaffold materials required for osteochondral tissue engineering, and they are expected to become a new type of scaffolds with gradient pore sizes for osteochondral repair.