Objective To clarify the mechanism of cancer treatment by detoxicating herbs JC724. Methods Colorectal cancer cell eukaryotic RNA expression change was analyzed usinghigh-throughput technique after HT-27 cell treated 1h by JC724, a kind of detoxicating herbs, which had a definiteinhibit ted effect to colorectal cancer in our previous studies. Results The effect of JC724 on colorectal cancer cells showed significant difference in 25 gene expression, which were claudin-4 genes and other mitochondrial metabolism genes, such as MT-CO1 and MT-CO2 gene, MT-ND4L, MT-ND1 and MT-ATP8P1 genes. There was a significant difference in the expression of 324 gene after HT-29 cell treated 1h by Spreading hedyotis herb, which was the “jun drug” in JC724, including 95 up-regulated genes and 229 down-regulated genes. The top up-regulated genes and top down-regulated genes associated with mitochondrial metabolism were MT-CO1, MT-CO2, MT-ND1, MT-ND2, MT-ND4L, MT-ATP8P1, BCL2L1and BBC3. Compared with the Spreading hedyotis herb group, there was detected significant differences in the expression of 126 genes in the JC724 group, including 47 up-regulated genes and 79 down-regulated genes. ConclusionsIt showed the characteristics of complex system, the integrity, non-additivity and multi-targetting in the treatment of tumor for Chinese medicine, and the main molecular mechanism is closely related to regulate mitochondrial metabolism in the treatment of cancer by detoxicating herbs JC724.