The invention belongs to the field of gene technology and medicine, and particularly relates to a marker for predicting prognosis of colon cancer and application of the marker. The marker for predicting prognosis of the colon cancer comprises autophagy-related lncRNA and/or autophagy-related mRNA markers, wherein the autophagy-related lncRNA is CASC9, PCAT6, AP006621.2, GS1-124K5.4, MIR4435-2HG, AL354993.2, AC048344.4, AC010973.2, AL590483.1, AL137782.1, STAG3L5P-PVRIG2P-PILRB, LINC00513, SNHG16 and AP001554.1; and the autophagy-related mRNA is GRID1, DAPK1, RAB7A, PELP1, ULK3 and WIPI2. The marker for predicting the prognosis of the colon cancer can be used for predicting the prognosis risk and survival rate of the colon cancer, provides a guidance basis for prognosis and health management of patients, and realizes individual accurate treatment.