Nanostructured Guinier–Preston (GP) zones are critical for the strength of Al-Mg-Si(-Cu) aluminum alloys. However, there are controversial reports about the structure and growth mechanism of GP zones. In this study, we construct several atomic configurations of GP zones according to the previous research. Then first-principles calculations based on density functional theory were used to investigate the relatively stable atomic structure and GP-zones growth mechanism. The results show that on the (100) plane, GP zones consist of {MgSi} atomic layers without Al atoms, and the size tends to grow up to 2 nm. Along the (100) growth direction, even numbers of {MgSi} atomic layers are more energetically favorable and there exist Al atomic layers to relieve the lattice strain. {MgSi}2Al4is the most energetically favorable GP-zones configuration, and the substitution sequence of Cu atoms in {MgSi}2Al4during the aging process is Al → Si → Mg. The growth of GP zones is accompanied by the increase in Mg and Si solute atoms and the decrease in Al atoms. Point defects, such as Cu atoms and vacancies, exhibit different occupation tendencies in GP zones: Cu atoms tend to segregate in the Al layer near the GP zones, while vacancies tend to be captured by the GP zones.