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Atom probe tomography (APT) coupling high-resolution transmission electron microscopy (HRTEM) was used to analyze the fraction and compositions of different nanoparticles in two-stage double peaks aging process of Al−Zn−Mg alloy. Al content is found to be closely related to the size of nanoparticles and it can be greater than ~ 50.0 at. % in the nanoparticle with the equivalent radius under ~ 3.0 nm. Correspondingly, Al content of the nanoparticle, with the equivalent radius over ~ 5.0 nm, is measured under ~ 40.0 at. %. Evolution from Guinier–Preston (G.P.) zone to η phase is a growing process where Mg and Zn atoms enter the nanoparticle, therefore rejecting Al atoms. G.P. zones can take up a number fraction of ~ 85.0 and ~ 22.7% of nanoparticles in the first and second peak-aged samples, respectively, and even in the over-aged (T73) sample, they can still be found. As aging time increases, fraction of η′ phases monotonically rises to the peak value (~ 54.5%) in the second peak-aged state and then drops, which is significant for the second hardness peak and directly proves their function as the transitional medium. In T73 state, ~ 63.3% nanoparticles compose of η phases, which were measured to still contain ~ 10.2 to ~ 36.4 at. % Al atoms.