Objective To explore the relationship between long non-coding RNA (lncRNA)-8439 and pluripotency factor nanog, and to investigate the potential effect of lncRNA-8439 on the growth of hepatoma carcinoma cells. Methods RNA-sequencing and bioinformatics tools were used to screen the differentially expressed lncRNA related to pluripotency factors (nanog, oct4 and sox2) in primary and metastatic tissues of hepatocellular carcinoma. The differentially expressed lncRNA levels were tested by real-time quantitative PCR (qPCR) in human hepatoma carcinoma cell lines, Hep3B and Huh7, and their corresponding suspended spheres. The potential of binding of lncRNA-8439 and nanog was determined using bioinformatics tools. Localization of lncRNA-8439 in the Hep3B and Huh7 cells was observed by fluorescence in situ hybridization. After knocking down lncRNA-8439, the expression levels of nanog in the Hep3B and Huh7 cells were detected by qPCR and Western blotting, and the growth status of suspended spheres was observed. After overexpressing lncRNA-8439, the expression levels of nanog were measured by qPCR and Western blotting in the two kinds of cancer cells. Results A total of 9 differentially expressed lncRNAs related to pluripotency factors were identified, while only lncRNA-8439 expression was significantly higher in the suspended spheres of two kinds of cancer cells compared with their corresponding adherent cells (both P<0.01). LncRNA-8439 had binding sites of nanog at its 3'end. LncRNA-8439 was located in the nucleus of the Hep3B and Huh7 cells but not in the cytoplasm. After knocking down lncRNA-8439, the RNA and protein expression levels of nanog were significantly reduced in the Hep3B and Huh7 cells (all P<0.01), and the number of suspended spheres was also reduced. After overexpressing lncRNA-8439, the RNA and protein expression levels of nanog were significantly up-regulated in the two kinds of cancer cells (all P<0.01). Conclusion LncRNA-8439 affects self-renewal ability of hepatoma carcinoma cells through up-regulating expression of pluripotency factor nanog, which may be the cause of invasion and metastasis of hepatocellular carcinoma.