Isatin and its analogues have been shown anticancer activity against various cancer cell lines via restrainting cancer cell proliferation and tumor growth. In this study, five different statistical methods such as MLR, PCR, FA-MLR, GA-MLR, and GA-PLS, were used to aquaire the Quantitative relevance between cytotoxicity activity and 37 isatinstructures. Quantitative structure activity models indicated that topological and gateway parameters have an adequate impact on the cytotoxic activity of the tested molecules. Among the applied QSAR models, GA-PLS and MLR gave significant results with high statistical quality for predicting the inhibitory activity of the molecules. Molecular docking studies of these compounds were also investigated, and promising results were obtained. There was a good correlation between QSAR and docking results. For the validity of the docking studies, molecular dynamics (MD) simulation was also done.