Background: To gain a better understanding of the molecular mechanisms of spinal cord injury and the effects of Neurotrophin-3, differentially expressed microRNAs (DEmiRNAs) and genes (DEGs) were analyzed. Methods: The miRNA transcription profile of GSE82195 and the mRNA transcription profile of GSE82196 including dorsal root ganglion (DRG) tissue samples of normal adult rat (none, n=6), 10 weeks post-pyramidotomy, intramuscular AAV-1 GFP (injury, n=6) and 10 weeks post-pyramidotomy, intramuscular AAV-1 prepro-neurotrophin-3 (NT-3, n=6) were downloaded from the Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/). Then, differentially expressed RNAs (DERs) including DEmiRNAs and DEGs were identified using limma. The noise-robust soft clustering of the intersection DERs was performed using Mfuzz package. Additionally, the integrated miRNAs–targets regulatory network was constructed using Cytoscape. Finally, the Comparative Toxicogenomics Database 2019 update (http://ctd.mdibl.org/) were used to search the central nervous system injury related pathway. Results: A total of 444 DERs including 382 DEGs and 62 DEmiRNAs were screened between group injury and group none whlie 576 DERs including 523 DEGs and 55 DEmiRNAs were screened between group NT-3 and group injury. Moreover, 80 intersections DERs were identified.Two clusters were obtained including cluster 1 (including rno-miR-3072, rno-miR-667-5p and so on) and cluster 2 (OPRL1, GHSR and so on). DREs in cluster 1 were firstly significantly downregulated in group injury and subsequently were significantly upregulated in group NT-3. DERs in cluster 2 were firstly upregulated in group injury and subsequently downregulated in group NT-3. OPRL1 and GHSR were enriched in the KEGG pathway of Neuroactive ligand-receptor interaction which is also found in the Comparative Toxicogenomics Database 2019 update. OPRL1 was involved in the chemical homeostasis and ion homeostasis while GHSR was related to the regulation of fatty acid metabolic process and regulation of cellular ketone metabolic process. Conclusion: DEmiRNAs rno-miR-3072 and rno-miR-667-5p and DEGs OPRL1 and GHSR might participate in the pathogenesis of neurological injury and the neurotrophin-3 treatment. Keywords: spinal cord injury, differentially expressed miRNA, differentially expressed gene, regulatory network, Neurotrophin-3