Coptidis rhizoma (CR; Huanglian in Chinese) has been used for the treatment of cancer in Chinese medicine, and recent studies have supported its use in cancer therapy. MicroRNAs (miRNAs) play an important role in the pathophysiology of human cancers. We examined alterations in the miRNA profile of hepatocellular carcinoma (HCC) cells after treatment with Coptidis rhizoma aqueous extract (CRAE). An on-chip microarray method was used to detect alterations in the expression profile of miRNAs in human HCC MHCC97-L cells after exposure to 175 μg/ml CRAE. Altered expression of several miRNAs was detected in the MHCC97-L cells after treatment with 175 μg/ml CRAE. The microarray results were validated by quantitative real-time PCR (qRT-PCR). Consistent results were obtained; qRT-PCR confirmed that both miR-21 and miR-23a were significantly up-regulated. TargetScan and PicTar microRNA databases were used to predict the possible target genes of the altered miRNAs. The results showed that the altered miRNAs after CRAE treatment may serve as markers for the therapy of liver cancer. To the best of our knowledge, this is the first report on the up-regulation of miRNAs, miR21 and miR23a in human liver cancer cells treated with CRAE. Our results suggest that CRAE targets miR-21 and miR-23a in liver cancer cells supporting the potential application of CRAE in the treatment of HCC.