Abstract: To investigate the chan ges of lncRNA expression profile and the mechanism of cis-regulation of lncRNA-mRNA during the inhibition of Biejiajianwan on Hepatocellular carcinoma cells, the proliferation activity of SMMC-7721 cells was detected by CCK8 method. LncRNA expression and characteristics were analyzed by whole-cell transcriptome, and the LncRNA-mRNA cis-regulation network was constructed. The results show ed that serum containing Biejiajianwan inhibited the proliferation of hepatocellular carcinoma cell lines.Whole-cel l t ranscriptomic analysis showed that 172 lncRNAs were differentially expressed. LncRNA-mRNA cis-regulation network was constructed and survival analysis of the regulatory genes showed that the expression of SCRN1, PLEKHA1, HNRNPM, TMEM107, ETNK1 and ISG20 L2 was significantly negatively（P＜0.05）. Consequently, it was concluded that LncRNA was involved in the process of inhibiting the proliferation of hepatocellular carcinoma cells in Biejiajianwan, and cis regulation of LncRNA-mRNA was one of its molecular mechanisms.