Epidemiological studies in different populations, in different countries, and in different epochs consistently showed that high intelligence is positively correlated with longevity. Despite the definitive association, the reason of the linkage between higher intelligence and longevity has remained unknown. Here, we show by using Drosophila melanogaster that both higher intelligence and longevity are genetically linked. The high intelligent D. melanogaster (INT) lived longer than non-intelligent flies (NINT), 26.40% and 21.35% in male and female, respectively. The bidirectional selective breeding based on intelligence extended lifespans gradually generation by generation in INT breeding and reverse in NINT breeding. The INT of F₁₂ generation lived longer than NINT of F₁₂ generation, 63.91% for male and 67.88% for female, as a result from slower aging. Whole-genome analysis showed that the genetic linkage of higher intelligence with longevity was determined by the genes of the pathways of ribosome, autophagy, and genome stability.