Abstract: In order to explore the rapid repair and growth mechanism of damaged deer antler and explore candidate genes related to repair growth, the antler tissues of the Cervus elaphus yarkandensis were collected at 53 days after injury repair（injured group） and 53 days after normal growth（normal group）. After total RNA was extracted, transcriptome sequencing was performed based on Illumina Nova Seq 6000 high-throughput sequencing platform. The filtered sequences were compared with the reference genome sequences and differentiated expression genes（differentially expressed genes, DEGs） were screened. GO functional enrichment analysis and KEGG signaling pathway enrichment analysis were performed on DEGs. Finally, four DEGs were randomly selected for real-time fluorescence quantitative PCR analysis to verify the reliability of transcriptome sequencing results. The results showed that there were 56 DEGs between injured group and normal group. Compared with the normal group, 37 DEGs in the injured group were significantly up-regulated（|lb Fold Change|≥1,P＜0.05）, including IHH, IL2RA, BVES, Wnt5B, COL9A2, CRMP5, etc., and 19 DEGs were significantly down-regulated（|lb Fold Change|≥1,P＜0.05）, including LOC122686105, ALX3, VWF, etc. In the injured group,there were 23 GO level 2 items that were significantly up-regulated（P＜0.05）, including 19 GO secondary entries（skeletal phylogeny GO:0001501, chondrogenesis GO:0051216, etc.） of biological process（BP）, 2 GO secondary entries（fibromyofilm GO:00042383, leap disk GO:0014704） of cellular component（CC） and 2 GO secondary entries（protein binding GO:0005515, same protein binding GO:0042802） of molecular function（MF）, and 8 GO secondary entries that were significantly down-regulated（P＜0.05）, including 7 GO secondary entries（including extracellular region GO: 0005576, chemical homeostasis GO: 0048878 of BP and bone growthGO:0098868） and 1 secondary entry（N-terminal binding of protein GO:0047485） of CC. In the injured group, 13 KEGG signaling pathways were significantly up-regulated（P＜0.05）, including Hedgehog signaling pathway, Wnt signaling pathway and steroid biosynthesis, and 9 KEGG signaling pathways were significantly down-regulated（P＜0.05）, including vitamin digestion and absorption, cholesterol metabolism and PPAR signaling pathway. Candidate genes associated with the pair growth of velvet antler were IHH, IL2RA, Wnt5b, COL9A2 and CRMP 5 in 56 DEGs. Real-time fluorescence quantitative PCR analysis showed that compared with the normal group, IHH, IL2RA and BVES genes were up-regulated significantly（P＜0.05）, while LOC122686105 gene was down-regulated significantly（P＜0.05）in the injured group, which was consistent with the quantitative results of DEGs transcriptome. These results indicate that the injured state could promote the development of skeletal system and cartilage of velvet antler, IHH, IL2RA, Wnt5B, COL9A2, CRMP5 and other genes might play a direct or indirect role in the rapid repair and growth process of velvet antler after injury.