Aging behavior and phase transformation of Al–5Zn–1Mg–1Cu(-Si) alloys under different isothermal temperatures were investigated using transmission electron microscope (TEM) and mechanical tests. The aging temperature and Si addition significantly influenced to the types of precipitated phases and mechanical properties of the Al–Zn–Mg–Cu alloys. Adding Si in this alloy changed the precipitated phases from T′ and η′ phases to the dual-sized η and GPB-II phases. With increasing isothermal aging temperature, more GPB-II phases formed in alloys with the same composition, effectively improving the microhardness and mechanical properties. When aging at 150 °C, 0.5 wt%Si-containing alloy reached the highest peak hardness of about 150HV and maintained stable hardness, while an alloy without Si only reached 120HV and later declined by 15HV. The tensile strength and yield strength of the 0.5 wt%Si-containing alloy were higher than those of non-Si alloy by 132 MPa and 165 MPa, increasing 51% and 90%, respectively. This result was due to the presence of fine and dispersed 4–8 nm GPB-II phases in 0.5 wt%Si-containing alloy. The GPB-II phase had a core-shell structure, with the core region mainly enriched in Mg and Si, and the shell region mainly enriched in Cu and Zn. Compared with the stability of T′ and η′ phases, this core-shell structure of GPB-II effectively inhibited its growth and beneficially maintained a smaller-sized GPB-II phase. The strengthening effect of GPB-II phase was better than that of η or T phases when aging at 150 °C or 200 °C. The mechanical properties of high Zn/Mg ratios Al–Zn–Mg–Cu alloys can enhanced by adding Si.