Intervertebral disc degeneration (IDD) is a progressive condition and stands as one of the primary causes of low back pain. Cell therapy that uses nucleus pulposus (NP)-like cells derived from human induced pluripotent stem cells (hiPSCs) holds great promise as a treatment for IDD. However, the conventional two-dimensional (2D) monolayer cultures oversimplify cell−cell interactions, leading to suboptimal differentiation efficiency and potential loss of phenotype. While three-dimensional (3D) culture systems like Matrigel improve hiPSC differentiation efficiency, they are limited by animal-derived materials for translation, poorly defined composition, short-term degradation, and high cost. In this study, we introduce a new 3D scaffold fabricated using medicalgrade chitosan with a high degree of deacetylation. The scaffold features a highly interconnected porous structure, near-neutral surface charge, and exceptional degradation stability, benefiting iPSC adhesion and proliferation. This scaffold remarkably enhances the differentiation efficiency and allows uninterrupted differentiation for up to 25 days without subculturing. Notably, cells differentiated on the chitosan scaffold exhibited increased cell survival rates and upregulated gene expression associated with extracellular matrix secretion under a chemically defined condition mimicking the challenging microenvironment of intervertebral discs. These characteristics qualify the chitosan scaffold-cell construct for direct implantation, serving as both a structural support and a cellular source for enhanced stem cell therapy for IDD.