Phenols and its analogues are known to induce caspase-mediated apoptosis activity and cytotoxicity on various cancer cell lines. In the current work, two types of molecular field analysis techniques were used to perform the three dimension quantitative structure activity relationship (3D-QSAR) modeling between structural characters and anticancer activity of two sets of phenolic compounds, which are comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Then two 3D-QSAR models for two sets of phenolic analogues were obtained with good results. The first QSAR model, which was derived from CoMFA for phenols with caspase-mediated apoptosis activity against L1210 cells, had good predictability (q² = 0.874, r² = 0.930), and the other one was derived from CoMSIA for electron-attracting phenols with cytotoxicity in L1210 cell (q² = 0.836, r² = 0.950). In addition, the CoMFA and CoMSIA contour maps provide valuable guidance for designing highly active phenolic compounds.