Non-small cell lung cancer (NSCLC) is one of the leading causes of cancer-related death, including two major pathologic subtypes, adenocarcinoma (AD) and squamous cell carcinoma (SCC). There are significant differences in the aberrant gene profiling and molecular characteristics among LUAD and LUSC, which lead to the different chemotherapeutic regimens administered to the two NSCLC subtypes. Therefore, unique genetic or epigenetic accurately distinguishing these two subtypes is critical for the diagnosis and treatment of patients. In this study, we tried to develop and validate novel long non-coding RNA (lncRNA)-based signatures to facilitate the diagnosis and individualized treatment of LUAD and LUSC. To analyze the distinct lncRNA profiling in LUAD and LUSC, the paired tissue samples of RNA sequencing or microarray data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) was used. We found that lncRNA expression pattern is different in LUAD and LUSC, and three up-regulated and down-regulated lncRNAs expressions in LUAD and LUSC tissues were validated. In addition, knockdown of the up-regulated lncRNA AFAP1-AS1 and LINC00511 impaired LUAD cell proliferation, while knockdown of PVT1 inhibited LUSC cell growth. Furthermore, four 6-lncRNAs signature expression patterns were found to be significantly associated with LUAD and LUSC patient overall and progression-free survival. Taken together, the different lncRNAs signature might accurately distinguish LUAD and LUSC and predict clinical outcome for these two different subtypes of NSCLC.