Colon cancer (CC) is the most common type of gastrointestinal cancer and is the third leading cause of cancer patient's death worldwide. Long non-coding RNAs (lncRNAs) are important regulatory molecules involved in various cellular processes, and many of them are shown as significant prognosis biomarkers of malignant tumors. In the present study, we identified differentially expressed lncRNAs between CC and adjacent normal tissues based on two TCGA database (GEPIA and circlncRNAnet). Over 1500 differentially expressed lncRNAs between CC and adjacent normal tissues were obtained based on these two websites, and 72 lncRNAs (FC > = 2, Log2 (TPM+1) > 1, P < 0.05) were chosen for further analysis. Seventeen of them were CC specific-expressed lncRNAs. We then evaluated the expression of the 17 lncRNAs in diverse tumor stage. LncRNA double homeobox A pseudogene 8 (DUXAP8), RP11-54H7.4, and RP11-138J23.1 showed higher expression in later tumor stages. Built on survival analysis, we found that high expression of DUXAP8 and ELFN1 antisense RNA 1 (ELFN1-AS1) predicts poor prognosis in CC. In addition, high expression of the 17 lncRNAs set predicts poor prognosis in CC. This study provides a new way to evaluate the prognosis of CC.