The anti-aging effects and possible molecular mechanisms of Phyllanthus emblica Linn. (PE) were investigated in this study. Results revealed that PE extracts increased antioxidant enzyme activities, total antioxidant capacity (T-AOC) levels, and decreased malondialdehyde (MDA) content in the serum and tissues of D-galactose (D-gal) mice. PE also improved the motor and learning memory abilities of D-gal mice. In addition, PE regulated the abundance of Firmicutes, Bacteroidota, and other bacteria in the gut microbiota of D-gal mice, affecting the tricarboxylic acid (TCA) cycle based on functional predictive analysis. The molecular docking and cellular thermal shift assay revealed that chebulic acid (CA, binding energy of −183.6289 kcal/mol) might be the key active substance in PE extract. Sirtuin 6 (Sirt6) is an important protein that affects aging and energy metabolism. Circular dichroism spectrum and Western blot analysis found that CA altered the secondary protein structure of Sirt6 and increased its deacetylase activity. Co-Immunoprecipitation assay results showed that Sirt6 and nuclear factor erythroid 2-related factor 2 (Nrf2) interacted in the presence of CA. Finally, Western blotting analysis found that PE extracts up-regulated the expression of Sirt6, Nrf2, and heme oxygenase-1 (HO-1) proteins in the tissues of D-gal mice. Overall, the phenolic acids of PE may regulate oxidative stress through the interaction of Sirt6, and affect the gut microbiota of mice. This study provided theoretical guidance for the potential application and the mechanism of health effects from PE.