The hydrogen trap sites and corresponding hydrogen binding energies in an Al–Cu–Mg alloy with the different microstructures were investigated to unravel the environmental hydrogen embrittlement (HE) behavior of the alloy. The results showed that hydrogen can reside at interstitial lattices, dislocations, S′-phase, and vacancies. In the aged specimen with the highest hydrogen content, it was firstly reported that hydrogen resided at S′-phase particles with relatively high binding energy, which is a determinant factor on HE resistance of the alloy. In the cold-rolled specimen, high content of hydrogen trapped at dislocations with a reversible nature leads to intergranular hydrogen-assisted cracking. In the solution-treated specimen, hydrogen migration to the surface due to low trap density results in low hydrogen content and prevents the GBs from reaching critical hydrogen concentration. The obtained results clearly reveal that trap site density, and the nature of trap sites can determine environmental HE susceptibility of the alloy.