Spinal cord injury (SCI) often leads to the loss of motor and sensory functions and is a major challenge in neurological clinical practice. Understanding the pathophysiological changes and the inhibitory microenvironment is crucial to enable the identification of potential mechanisms for functional restoration and to provide guidance for the development of efficient treatment and repair strategies. To date, the implantation of specifically functionalized biomaterials in the lesion area has been shown to help promote axon regeneration and facilitate neuronal circuit generation by remolding SCI microenvironments. Moreover, structural and functional restoration of the spinal cord through the transplantation of naive spinal cord tissue grafts from adult donors, artificial spinal cord-like tissue developed from tissue engineering, and 3D printing will open up new avenues for SCI treatment. This review focuses on the dynamic pathophysiological changes in SCI microenvironments, biomaterials for SCI repairs, strategies for restoring spinal cord structure and function, experimental animal models, regenerative mechanisms, and clinical studies for SCI repair. The current status, recent advances, challenges, and prospects of scaffold-based SCI repair from basic to clinical settings are summarized and discussed, to provide a reference that will help to guide the future exploration and development of spinal cord regeneration strategies.