This study investigated the mechanism of neurotrophin-3 (NT-3) in promoting spinal cord injury repair through the transforming growth factor-beta (TGF-β) signaling pathway. A mouse model of spinal cord injury was established. Forty C57BL/6J mice were randomized into model, NT-3, NT-3 + TGF-β1 and NT-3 + LY364947 groups. The Basso–Beattie–Bresnahan (BBB) scores of the NT-3 and NT-3 + LY364947 groups were significantly higher than the model group. The BBB score of the NT-3 + TGF-β1 group was significantly lower than NT-3 group. Hematoxylin-eosin staining and transmission electron microscopy showed reduction in myelin sheath injury, more myelinated nerve fibers in the middle section of the catheter, and relatively higher density and more neatly arranged regenerated axons in the NT-3 and NT-3 + LY364947 groups compared with the model and NT-3 + TGF-β1 groups. Immunofluorescence, TUNEL and Western blot analysis showed that compared with model group, the NEUN expression increased, and the apoptosis and Col IV, LN, CSPG, tenascin-C, Sema 3 A, EphB2 and Smad2/3 protein expression decreased significantly in the NT-3 and NT-3 + LY364947 groups; the condition was reversed in the NT-3 + TGF-β1 group compared with the NT-3 group. NT-3 combined with TGF-β signaling pathway promotes astrocyte differentiation, reduces axon regeneration inhibitory molecules, apoptosis and glial scar formation, promotes axon regeneration, and improves spinal cord injury.