Objective To detect changes in microRNA and target mRNA at the head and tail of the corticospinal tract (CST) injury side, and to investigate the function of microRNA in spinal cord injury (SCI) and repairment, which could provide a theoretical basis and experimental evidence in regeneration of the CST after injury.Methods The left side of the CST in 30 rats was cut at the level of the pyramid of medullar oblongata. The BBB test was used to assess the motor function. After the CST injury, the bioinformatics method was conducted to screen differences in microRNA target gene prediction. The intersection of differentially expressed mRNA was selected to conduct the microRNA and mRNA co-expression analysis. Real-time PCR was applied to detect the gene expression of miR-342-5p and Irf8 in 12 rats. Western blotting was applied to detect the protein expression of Irf8 and Iba1 in 6 rats. Results The limb movement after CST semitransection was uncoordinated, and motor function was limited according to BBB test but not completely paralyzed. There were statistical significances(P<0.05)after comparing 2 hours, 1 day, 3 days, 5 days and 7 days with the control group, indicating the successful establishment of model. Comparison of the inrostraland caudal region between 2 hours and 5 days, we focused on biological processes in regeneration. Data analysis from Realtime PCR experiments indicated that caudal miR-342-5p expression was significantly different(P<0.01) from 2 hours to 5 days, with a reverse correlation with Irf8 expression, whereas no change was observed in rostral miR-342-5p(P>0.05). Real-time PCR data analysis showed that the expression of Irf8 was consistent with the chip result , statistically significant difference compared with control groups (P<0.01). The result of Western blotting indicated that, comparing tissue from 5 days with 2 hours, both Irf8 and Iba1 were significantly creased in caudal samples (P<0.01). Conclusion After CST injury, there were significant up-regulated or down-regulated differentially expressed genes in rostral and caudal regions. In the caudal region, the miR-342-5p and Irf8 reverse expression and miR-342-5p was closely related to SCI repair and regeneration by glial cell activation.