Intervertebral disc (IVD) degeneration is one of the most important causes of lower back pain. Tissue engineering provides a new method for the experimental treatment of degenerative disc diseases. This study aims to develop a natural, acellular, 3D interconnected porous scaffold derived from the extracellular matrix (ECM) of nucleus pulposus. The nucleus pulposus (NP) was decellularized by sequential detergent-nuclease methods, including physical crushing, freeze-drying and cross-linking. These 3D porous scaffolds were fabricated with a high porosity of (81.28 ± 4.10)%, an ideal pore size with appropriate mechanical properties. Rabbit bone marrow mesenchymal stem cells (rBMSCs) were seeded and cultured on the scaffolds. And the mechanical tests showed the compressive elastic modulus of the scaffolds cultured for 4 weeks reached 0.12 MPa, which was better than that of the scaffolds cultured for 2 weeks (0.07 MPa) and that of the control group (0.04 MPa). Scanning electron microscopy (SEM), histological assays, molecular biology assays revealed that the scaffolds could provide an appropriate microstructure and environment for the adhesion, proliferation, migration and secretion of seeded cells in vitro. As assays like histology, immunohistochemistry and the real-time qRT-PCR showed, NP-like tissues were preliminarily formed. In conclusion, the 3D porous scaffold derived from NP ECM is a potential biomaterial for the regeneration of NP tissues.