Botanically derived natural products have recently become an attractive source of new chemotherapeutic agents. To explore active anticolorectal cancer compounds, we carried out phytochemical studies on Alkanna tinctoria and isolated eight quinone compounds. Using different spectral methods, compounds were identified as alkannin (1), acetylalkannin (2), angelylalkannin (3), 5-methoxyangenylalkannin (4), dimethylacryl alkannin (5), arnebifuranone (6), alkanfuranol (7), and alkandiol (8). Compounds 4, 7, and 8 are novel compounds. The structures of the three novel compounds were elucidated on the basis of extensive spectroscopic evidence including high-resolution mass spectrometry and nuclear magnetic resonance spectra. The antiproliferative effects of these eight compounds on HCT-116 and SW-480 human colorectal cancer cells were determined using the MTS method. Cell cycle and apoptosis were determined using flow cytometry. Enzymatic activities of caspases were determined using a colorimetric assay, and interactions of compound 4 and caspase 9 were explored by docking analysis. Among the eight compounds, alkannin (1), angelylalkannin (3), and 5-methoxyangenylalkannin (4) showed strong antiproliferative effects, whereas compound 4 showed the most potent effects. Compound 4 arrested cancer cells in the S and G2/M phases, and significantly induced cell apoptosis. The apoptotic effects of compound 4 were supported by caspase assay and docking analysis. The structural-functional relationship assay suggested that to increase anticancer potential, future modifications on alkannin (1) should focus on the hydroxyl groups at C-5 and C-8.