The microstructure evolution and strengthening ability of natural aging (NA), delayed aging (DA), and DA after pre-aging (PDA) of Al−Mg−Si alloy were studied. Results show that small and unstable atomic clusters are generated during NA, leading to the formation of low-density coarse βʺ and β′ phases, thus reducing the strength of DA alloy. However, atomic clusters and GP zones with larger sizes and high Mg/Si molar ratio form during pre-aging treatment. They prevent the generation of clusters during NA and can serve as effective nucleation sites in subsequent artificial aging, which elevates the number density of fine βʺ precipitates and improves the alloy strength. After pre-aging at 175 °C, the strengthening capacity of PDA alloy is restored, with hardness and yield strength reaching  95.1% and 101.9% of peak-aged alloy.