Nanoclusters formed during natural aging cause the negative effect of the two-step aging in the age-hardenable Al-Mg-Si alloys. The relationship between the clustering behavior during natural aging and the two-step aging behavior was studied using the hardness, differential scanning calorimetry (DSC), electrical resistivity measurements, transmission electron microscopy (TEM) observation in the Cu-free and Cu-added Al-Mg-Si alloys. Three stages during the two-step aging are clearly revealed based on the hardness results. The hardness in the two-step aging with the natural aging time is decreased, increased and then decreased at the initial, middle and final stages, respectively. Si-rich clusters initially formed during natural aging do not transform into the β′′ phase and are thermally stable during the two-step aging at 170°C. On the other hand, Mg-Si co-clusters formed at the middle stage during natural aging transform into the β′′ phase and are thermally unstable during the two-step aging at 170°C. Much higher hardness is obtained in the Cu-added alloy than that of the Cu-free alloy during two-step aging when natural aging is performed for 3.6 ks belonging to the initial stage. The higher hardness is also found to be obtained during over-aging regardless of the natural aging time in the Cu-added alloy than that of the Cu-free alloy. The relationship between the clustering behavior during natural aging and the two-step aging behavior is discussed based on the observed age-hardening phenomena.