A spinal cord hemisection injury model was established in rats. Treatment with IN-1 and/or neurotrophin-3 was found to regulate the expression of growth-associated protein 43, nerve growth factor, and basic fibroblast growth factor genes in the injured spinal cord tissues; transcript levels were first increased and then decreased. Expression levels reached a peak at days 7 (growth-associated protein 43) or 14 (nerve growth factor and basic fibroblast growth factor) following spinal cord injury. Combined treatment with neurotrophin-3 and IN-1 achieved the most apparent effect on the expression and recovery of motor function. These findings confirm that combined therapy with neurotrophin-3 and IN-1 can increase expression of growth factors in the injured spinal cord tissues and promote the axonal regeneration.