The clustering behavior during natural aging (NA) and subsequent artificial aging (AA) at 170°C in Al–Mg–Si alloys with the different Mg/Si ratio is evaluated using three-dimensional atom probe (3DAP). The internal composition of clusters formed during short-term NA is strongly associated with the alloy composition and prolonged NA leads to the formation of clusters with a Mg : Si ratio close to 1. The number density of clusters decreases with no dependence on the cluster size, and Si-rich clusters with Mg/(Mg+Si) values inside clusters below 0.4 show little variation during AA for 1.2 ks. It is believed that Mg–Si clusters with ranging from 0.4 to 0.6 in the Mg/(Mg+Si) value inside clusters can both dissolve and grow during AA. It is revealed that the delay in age hardening in the early stage of AA is closely related to the number density of the Si-rich and Mg–Si clusters.