Objective To analyze the expression changes of related mRNA and microRNA（miRNA）during spinal cord regeneration after tail amputation of Gekko japonicus, and to explore the biological effects of differentially expressed mRNA and miRNA during spinal cord regeneration.   Methods Fifty Gekko japonicus, the tail amputation model of Gekko japonicus was constructed, divided into normal group, 15days tail amputation group, and 25days tail amputation group, 5 in each group, repeat the experiment 3 times, 5 spare. Samples of each group were collected, RNA of each group was extracted and high-throughput sequencing. Bioinformatics analysis identifies differentially expressed mRNA and miRNA between groups, Gene Ontology(GO) enrichment analysis of differentially expressed mRNA functional annotations, and construction of miRNA and mRNA gene regulatory networks related to spinal cord regeneration.   Results The differential expression of mRNA and miRNA in the normal and newborn spinal cords of Gekko japonicus was analyzed by sequencing. The 15days and 25days tail amputation groups identified 538 and 510 differential mRNA expressions and 446, 127 differential miRNA expressions, respectively. GO analysis found that the differentially expressed mRNA aggregated in biological processes related to cell proliferation and neurodevelopment. In the spinal cord regeneration-related miRNA and its target gene regulatory network, 21 mRNA expression was down-regulated in the 15days tail amputation group, which was regulated negatively by 41 up-regulated miRNAs; 12 mRNA expression was up-regulated and was regulated by 29 down-regulated miRNAs. In the 25days tail amputation group, 8 mRNA expression was down-regulated and regulated negatively by 10 up-regulated miRNAs; 20 mRNA expression was up-regulated and regulated by 32 down-regulated miRNAs.   Conclusion Through the analysis of the differential expression of miRNA and mRNA in the regenerated spinal cord of Gekko japonicus, the expression changes of mRNA and miRNA in spinal cord regeneration were initially revealed, which provided experimental data for elucidating the molecular mechanism of spinal cord regeneration.