The intestinal flora serves as a crucial regulator of healthy aging. As individuals age, the composition and function of the intestinal flora undergo substantial alterations, which are closely linked to various aging-related diseases. This article summarizes the changes in intestinal flora associated with aging and explores the potential of natural foods to ameliorate aging-related diseases via intestinal flora intervention. Specifically, interventions from natural food sources such as probiotics, prebiotics, appropriate dietary supplements, and nutritional intake have shown beneficial effects on improving gut health and delaying the aging process. The article further discusses the impact of various dietary patterns and nutritional restrictions on the intestinal flora composition and lifespan extension. Finally, the article summarizes key findings of intestinal flora in nutritional intervention studies involving intestinal flora and aging, providing evidence and future guidance for further exploring the potential intestinal flora intervention in anti-aging strategies.