In order to improve the structure and function of acute spinal cord injury, the present study investigated the effect of electro-acupuncture (EA) on the differentiation of mesenchymal stem cells (MSCs) and the regeneration of nerve fibers in transected spinal cord of rats. The differentiation of MSCs into neuron-like cells and neuroglial cells and regeneraton of 5-hydroxytrptamine (HT) nerve fibers in the injured site of spinal cord were assessed after treatment with EA, MSCs transplantation, and EA plus MSCs transplantation. Compared with the control and MSCs groups, the content of endogenous neurotrophin-3 (NT-3) in the injured site and nearby tissues was increased in EA and EA+MSCs group. The differentiation of MSCs into neuronal-like cells and oligodendrocyte-like cells and number of 5-HT positive nerve fibers in the injured site were enhanced in the EA+MSCs group. Basso, Beattie, Bresnahan score of the paralyzed hindlimbs was highest in the EA+MSCs group. The present study demonstrates that electro-acupuncture can promote the differentiation of MSCs and regeneration of nerve fibers in injured spinal cord through induction of endogenous NT-3, and that combination of EA and MSCs transplantation can improve partial function of paralyzed hindlimbs.