While plate-like Guinier-Preston (GP) zones are formed during aging process in Al-Cu alloys, spherical nanocluster formation occurs in the early stage of aging in Al-Mg-Si alloys. Unlike well-known GP (I) zone in Al-Cu, there is no specific configurations within the nanocluster. However, the solute concentration and local configuration should play decisive role in subsequent formation of precipitates. In the present study, the first-principles calculations were performed to investigate the factors determining the stable shape during the formation process of GP zones and clusters in Al-Cu and Al-Mg-Si alloys. As a result of formation energy calculation of three-body bonds, the Cu-Cu-Cu triplet with the bond angle of 90° was the most stable. Monte Carlo simulations with newly developed machine-learning potential were then performed, and consequently the segregation of Cu atoms with the bond angle of 90° was observed more frequently. In contrast, three-body triplet with the bond angle of 60°was most stable without any specific directional anisotropy in Al-Mg-Si alloy, resulting in the formation of spherical nanoclusters. These results suggest that the intrinsic feature of the stability of local bonding dominates the shape of GP zones and nanoclusters, in which planar- or spherical-like cluster is formed.