This study aimed to investigate the anti-aging effects of black rice-anthocyanin (BRA) in Drosophila melanogaster and HUVEC cells. In this study, the strong antioxidant activity of BRA in HUVEC cells, D. melanogaster of lifespan extension, and molecular mechanism were elucidated. Firstly, the BRA increased enzyme activities of superoxide dismutase (SOD) and catalase (CAT), as well as the expression of phosphatidyl inositol 3-kinase (PI3K)/protein kinase B (Akt) protein while decreasing the accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA) in both H2O2-induced HUVEC cells and D. melanogaster. Secondly, the BRA extended the lifespan of D. melanogaster by improving crawling ability and intestine abilities in the microbial environment, barrier function, and number of autophagic lysosomes, as well as inhibiting the abnormal multiplication of stem cells in the intestine. Thirdly, the BRA downregulated expression levels of Akt-1 and mTOR in D. melanogaster while upregulated downstream autophagy gene expression levels of Atg1, Atg5, Atg8a, and Atg8b, as well as the expression levels of SOD, CAT, and 4E-binding protein. Lastly, the anti-aging mechanism was also verified by both the computerized molecular simulation and network pharmacology. Thus, the prolonged lifespan of D. melanogaster by blocking the mTOR pathway and activating autophagy, which could be further used for improving health and prolonging life.