Objective. In traditional Chinese medicine (TCM), chronic myeloid leukemia (CML) has been attributed to “poisoned bone marrow,” which is viewed as a loss of Qi or blood, a deficiency in Yin or Yang that causes a complex imbalance between cell growth and death. Malignant myeloid progenitor cells display excessive growth that is difficult to control without toxicity. More than 60 herbs in TCM have shown efficacy against CML. However, the key molecules and mechanisms involved in the holistic-level characterization, as well as the effective target associations, are still unknown. Methods. The present study employed a computational approach with filtering potential compounds via admetSAR, systems biology-based functional data prediction, and biochemical and molecular biological validation. Results. We generated 118 bioactive compounds from 11 herbs within four dialectical therapy groups that are most commonly used to treat CML and predicted 141 potential targets. The stilbene resveratrol and its derivatives were found to be highly related to these targets. Among them, α-viniferin was predicted to target Bcl-2, caspase-3, 8, and 9, MAPK14, CDK2, HSP90AA1, and others, reflecting CML therapeutic strategies. In vitro, experimental data showed a nonnecrotic growth limitation of K562 cells caused by α-viniferin, with an IC50 of 13.61 μg·mL−1 at 24 h. Finally, we validated the chemotherapeutic effect of α-viniferin in association with a mitochondria-driven apoptotic mechanism and in sequences entailing mitochondrial dysfunction, which had attributed to the expression of the proapoptotic Bcl-2 protein and executed K562 cell apoptosis. Conclusions. Our work sheds light on the mechanism of the efficacy of the stilbene α-viniferin in TCM for the prevention of CML. This work also predicts and validates targets in the mitochondrial signaling pathway, providing a novel strategy for CML treatment.