Aims: Both the SOX9 gene and bone marrow mesenchymal stem cells (BMSCs) have been applied for regeneration of degenerated intervertebral discs (IVDs) in animal models. However, whether the combined application of the SOX9 gene and BMSCs improves the regeneration of IVDs has yet to be investigated. Materials and methods: In this study, recombinant adenovirus Ad-SOX9-GFP and Ad-GFP control were prepared and used to transfect BMSCs that were labeled with the red CM-DiI tracer. After establishing the IVD degeneration (IDD) rabbit model by aspirating the nucleus pulposus in L2-3, L3-4, and L4-5, a composite alginate hydrogel containing 2.5x10(7) recombinant BMSCs/ml was injected into these intervertebral spaces. During the 4th, 24th, and 48th weeks, the experimental animals were subjected to histological and morphological observation, spine X-ray imaging, MRI imaging, and IVD height index (DHI) calculation. Results: H&E staining showed that the BMSCs grew well and were evenly distributed in the IVD tissues. During the 48th week, immunohistochemical staining showed that there was more type II collagen expression in the IVD tissue of the experimental group than in the control group. Imaging showed that both the DHI values and the MRI T2 signals in the experimental group were significantly higher than those in the controls. Conclusion: BMSCs expressing the SOX9 gene can significantly delay reduction of disc height and to some extent reverse degeneration of intervertebral discs in the rabbit IDD model, possibly through induction of BMSC differentiation into cartilage. These results suggest potential clinical applications of this novel strategy for treating IDD.