Long non-coding RNA (IncRNA) plays an important role in tumorigenesis. However, the expression pattern and function of IncRNAs in laryngeal squamous cell carcinoma (LSCC) are still unclear. To investigate the aberrantly expressed IncRNAs and mRNAs in advanced LSCC, we screened IncRNA and mRNA expression profiles in 9 pairs of primary Stage IVA LSCC tissues and adjacent non-neoplastic tissues by IncRNA and mRNA integrated micro-arrays. Gene Ontology and pathway analysis were performed to find out the significant function and pathway of the differentially expressed mRNAs, gene-gene functional interaction network and ceRNA network were constructed to select core mRNAs, and IncRNA-mRNA expression correlation network was built to identify the interactions between IncRNA and mRNA. qRT-PCR was performed to further validate the expressions of selected IncRNAs and mRNAs in advanced LSCC. We found 1459 differentially expressed IncRNAs and 2381 differentially expressed mRNAs, including 846 up-regulated IncRNAs and 613 down-regulated IncRNAs, 1542 up-regulated mRNAs and 839 down-regulated mRNAs. The mRNAs ITGB1, HIFI A, and DDIT4 were selected as core mRNAs, which are mainly involved in biological processes, such as matrix organization, cell cycle, adhesion, and metabolic pathway. LncRNA-mRNA expression correlation network showed LncRNA NR_027340, MIR31HG were positively correlated with ITGB1, HIF1A respectively. LncRNA SOX2-OT was negatively correlated with DDIT4. qRT-PCR further validated the expression of these IncRNAs and mRNAs. The work provides convincing evidence that the identified IncRNAs and mRNAs are potential biomarkers in advanced LSCC for further future studies.