Neuronal loss following spinal cord injury (SCI) remains a significant barrier to the recovery of neural function. Neural stem cells (NSCs) supplementation offers a promising therapeutic avenue by providing seed cells; however, the differentiation rate of NSCs into neurons is often suboptimal. In this study, lithium was immobilized on the surface of ZnO nanoparticles using a polydopamine coating to synthesize Li-PDA@ZnO nanoparticles. These nanoparticles were designed to induce NSC differentiation into neurons in a spatiotemporal-controlled manner using ultrasound-driven stimulation. Additionally, a biohydrogel system consisting of genipin and collagen was developed to encapsulate NSCs preloaded with endocytosed nanoparticles. The application of ultrasound stimulation to ZnO nanoparticles enhanced the differentiation of NSCs into neurons in a concentration-dependent manner following endocytosis. Li-PDA@ZnO nanoparticles demonstrated improved biocompatibility and further promoted neuronal differentiation, a process mediated by molecular pathways involving ERK and ASCL1. In vivo, the ability of ultrasound-driven nanoparticles to enhance NSC differentiation was validated using a mouse SCI contusion model. Furthermore, the combined nanoparticle-biohydrogel system was evaluated in an SCI transection model, where it was found to reduce local inflammation, enhance neuronal differentiation of NSCs, and increase the proportion of functional neurons. These effects contributed to significant improvements in motor, sensory, and autonomic function recovery following SCI. In summary, spatiotemporal-controlled ultrasound-driven Li-PDA@ZnO nanoparticles effectively enhance the differentiation of NSCs into neurons and, when incorporated into hydrogel systems, represent a novel therapeutic approach for spinal cord injury repair.