Objective To explore the effects of human urine-derived stem cells (hUSCs) and hUSCs combined with chondroitinase ABC (chABC) on the expressions of nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF) in the spinal cord injury (SCI) of rats, and to investigate the underlying mechanism. Methods hUSCs were cultured from human urine, and their phenotypes were detected by flow cytometry. The SCI model of rats were made via Allen method. Sixty Sprague Dawley rats were divided into 5 groups (n=12): the sham operation group (group A), SCI group (group B), SCI+hUSCs group (group C), SCI+chABC group (group D), and SCI+hUSCs+chABC group (group E). Basso, Beattie, Bresnahan (BBB) score was used to measure the lower extremity motor function of rats in each group at 10, 20, and 30 days after operation. Real-time fluorescent quantitative PCR was used to detect the relative mRNA expressions of NGF and BDNF at 30 days. Meanwhile, the protein expression of NGF and BDNF were confirmed by immunohistochemistry staining. The relative protein expressions of Bax and Bcl-2 were detected by Western blot. Results The hUSCs were identified to have multipotential differentiation potential. At 10, 20, and 30 days, BBB score was significantly lower in group B than in groups A, C, D, and E, in groups C, D, and E than in group A, in groups C and D than in group E (P<0.05). Real-time fluorescent quantitative PCR and immunohistochemistry staining demonstrated that the expressions of NGF and BDNF were significantly lower in group B than in groups A, C, D, and E, in groups C, D, and E than in group A, in groups C and D than in group E (P<0.05); but there was no significant difference between groups C and D (P>0.05). Western blot results indicated that the protein expression of Bax was significantly higher in group B than in groups A, C, D, and E, in groups C, D, and E than in group A, in groups C and D than in group E (P<0.05). Meanwhile, the protein expression of Bcl-2 was significantly lower in group B than in groups A, C, D, and E, in groups C, D, and E than in group A, in groups C and D than in group E (P<0.05). Conclusion hUSCs can protect SCI and this positive effect can be enhanced by chABC; this neuro-protective effect may depend on promoting the expressions of NGF and BDNF, and suppressing the neuronal apoptosis.