Background: Immune rejection is still the main cause of transplant failure of corneal transplantation which mechanism is not fully understood. The purpose of this study is to investigate the differential expression of long noncoding RNAs (lncRNAs) in corneal allograft rejection and to construct a network diagram of the interaction between lncRNAs and microRNAs(miRNAs). Methods: The lncRNAs expression profile of rat corneal transplantation was constructed by high throughput sequencing. The co-expressed mRNA was analyzed by gene ontology (GO), gene and genomic Kyoto encyclopedia (KEGG). An interaction network diagram of lncRNAs, miRNA and rejection related target genes was constructed. Part of the prediction was verified by real-time polymerase chain reaction (qPCR). Results: A total of 285 lncRNAs expressions were detected between the normal group and the autograft group, with 239 lncRNAs significantly upregulated and 46 lncRNAs downregulated, while 162 lncRNAs were upregulated and 20 downregulated between the allograft group and the autograft group. Go and KEGG were used to enrich and analyze the co-expression of mRNA. By analyzing the interaction between lncRNAs, miRNAs and target genes related to corneal allograft rejection, 56 upregulated lncRNAs,7 downregulated lncRNAs, 6 upregulated miRNAs and 4 downregulated miRNAs were found in allograft and autograft group. Three of the possible pathways were confirmed and verified by qPCR . Conclusions: The results showed that there was a difference in lncRNA expression between normal ,autograft and allograft group. LncRNAs may be a new molecular target in the treatment of corneal injury and corneal allograft rejection by interact with miRNAs.