Long non-coding RNA (lncRNA) plays important roles in many diseases, including pulmonary hypertension. The anti-diabetic drug metformin has been discovered to have protective effect on experimental pulmonary artery hypertension (PAH). However, the exact mechanism of metformin on the expression of lncRNA in PAH remains unclear. Here, we applied microarray analysis to examine lncRNA and mRNA expression proflies in pulmonary arteries (PAs) tissues of PAH rats with or without metformin treatment. A total of 24 lncRNAs (14 upregulated and 10 down-regulated) and 82 mRNAs (17 upregulated and 65 down-regulated) were differently expressed in PAH rats induced by MCT, whereas 83 lncRNAs (59 upregulated and 24 down-regulated) and 145 mRNAs (110 upregulated and 35 down-regulated) were differently expressed after metformin treatment. The expression levels of lncRNAs (NONRATT015587.2, NONRATT006975.2, NONRATT031226.2 and NONRATT024291.2 et al) were verified through realtime-PCR, and the results of NONRATT015587.2 and NONRATT024291.2 were consistent with RNA sequencing. Bioinformatics analysis was performed, including gene ontology (GO) analysis and genomes (KEGG) analysis. Transcription factor (TF)-target network analysis revealed that metformin regulated gene expression potentially via TFs including Tp53, Est1, Sp1 and Hif1α. The analysis illustrated that overexpression of NONRATT015587.2 promoted proliferation and knockdown of NONRATT015587.2 increased apoptosis of pulmonary artery smooth muscle cells in vitro, both of which were implicated in vascular remodeling in PAH. In addition, we found that the p53 and Hif1α signaling pathways may be involved in this regulation process. NONRATT015587.2 can be expected as a novel candidate in diagnostic markers for PAH. Our results provide novel insight into the mechanisms of the pivotal lncRNA-mRNA interactions, and indicate that NONRATT015587.2 acts as a pro-proliferative factor in regulation of pulmonary vascular remodeling.