Medicinal herbs are the preferred candidates for drug discovery against human diseases including cancer. The roots of Prismatomeris connata have been used in traditional herbal medicine to treat many health problems, particularly pneumoconiosis. This study was to test the anti-tumor activity of 3-Hydroxy-1,5,6-trimethoxy-2-methyl-9,10-anthraquinone (PCON6), a major anthraquinone derivative from C. connata, against lung cancer. Cell viability in cultures was assessed by MTT assay. Cell death or apoptosis was determined with Annexin-V and 7-Aminoactinomycin D staining. Cell cycle was analyzed by both propidium iodide DNA staining and BrdU incorporation assay. Here we showed that in a panel of fifteen different tumor cells lines, a group of four non-small cell lung carcinoma (NSCLC) cell lines exhibited a relatively higher sensitivity to PCON6 growth inhibition than the rest of most non-lung cancer cell lines (p = 0.0461). Further studies demonstrated that the suppression of NSCLC H520 cell growth by PCON6 was associated with its induction of apoptosis at 20 ${mu}M$ (p = 0.0008), and of cell accumulation at S phase cell cycle (p < 0.05) that was further supported by a decrease in cdc2 protein expression. This preliminary study suggests that natural compound PCON6 has relatively selective cytotoxicity against NSCLC growth and represent a concept of developing a novel drug therapy specific for NSCLC based on the roots of C. connata or PCON6.