The Si-modified Guinier-Preston-Bagaryatsky (GPB) zones are claimed to be responsible for the high-thermal stability of Al-Cu-Mg-Si alloys with a low Cu/Mg ratio. However, the structure of this phase and its formation mechanism remain unclear. In the present study, the precipitation behaviors of two Al-Cu-Mg alloys with or without Si addition upon thermal aging at 200 °C are characterized using atomic-resolution imaging techniques and the ab initio calculation. It is found that the Si-modified GPB zone is needle-shaped β'/GPB composite with core/shell structure. The core part is β' phase (Mg9Si5), while the shell is composed of the conventional GPB zones. In the early stage of aging, β' phase precipitates rapidly and acts as the heterogeneous nucleus of GPB zones. With the aging time extending to 60 h, the diameter of the β'/GPB composites remains almost constant, since the GPB zones effectively hinder the coarsening of the internal β' phase, thus promoting the thermal stability of the alloy as compared with the Si-free alloy. Our results clarify the mechanism of Si, at atomic scale, to improve the thermal stability of Al-Cu-Mg alloys with a low Cu/Mg ratio.