Cancer remains a significant global public health concern. Numerous challenges still remain in its treatment. Recently, a novel two-dimensional material—violet phosphorene nanosheets (VPNS)—has shown considerable application potential in the biomedical field due to its unique physicochemical properties. The VPNS with a concentration of 41.00 μg/mL has been demonstrated to exhibit significant anti-cancer effects through the induction of apoptosis. The treatment of VPNS was revealed by cell metabolomics analysis to a marked down-regulation of succinate hemialdehyde expression and an up-regulation of pyridoxine levels in cancer cells. These differentially expressed metabolites are closely associated with the vitamin B6 metabolic pathway. In addition, the VPNS has also been demonstrated to exert excellent anti-cancer effects within a living organism by in vivo animal experiments.