This study addresses the challenges of osteochondral tissue engineering by developing a hybrid scaffold with intercalated layers of poly(ε-caprolactone) (PCL) in combination with different concentrations of nanosized synthetic smectic clay (Lap) and a hydrogel of chitosan, collagen and demineralized bone powder (DBP). The scaffold design specifically targets the critical junction between subchondral bone and calcified cartilage and utilizes the mechanical strength of PCL/Lap nanocomposites and the bioactivity of the chitosan/collagen/DBP hydrogel to support tissue regeneration. The PCL/Lap nanocomposite, characterized by increased hydrophilicity, improved swelling behavior, and enhanced stiffness, provides a robust scaffold, while the hydrogel layers improve bioactivity and fluid retention. Three-dimensional printing technology was used to fabricate multi-layer scaffold, ensuring interfacial cohesion between the layers. Rheological, morphological, chemical, and mechanical characterizations confirmed the successful integration of the materials and the mechanical suitability for the subchondral environment. Biocompatibility assays demonstrated the non-hemolytic nature of the scaffolds and a favorable trend in cell viability with increasing Lap content. This study presents a novel scaffold design that effectively combines mechanical stability and biological functionality. It fulfills the complex requirements of osteochondral repair and offers a promising platform for future tissue engineering strategies.