To investigate the clinical efficacy of autologous bone marrow mesenchymal stem cells transplantation in patients with acute spinal cord injury. The clinical manifestations of these patients are abnormal sensation and motor functions that dominated by damaged nerve segment. A total of 36 patients with acute spinal cord injury were randomly divided into control group (n=18, treated with decompression + internal fixation + conventional medical treatments) and experimental group (n=18, control group’s treatment + autologous bone marrow mesenchymal stem cells injection in the subarachnoid space). The total effective rate in the observation group was higher than control group (P=0.045). After 12 months of treatment, the SCIM-III score, ASIA exercise score, Botsford score, and ASIA sensory score were significantly higher than those before treatment in both groups, and the increase in the observation group was more obvious (P<0.05). The time for muscle strength and muscle function recovery and independent walking in the observation group were less than those of the control group (P<0.05). Autologous bone marrow mesenchymal stem cells transplantation can improve the therapeutic effect and nerve function, promote the recovery of motor function, sensory function and spinal cord injury without disorder in humoral immune function.