•Atomic-structures of hardening precipitates in an Al-Mg-Si-Sc alloy are revealed.•Disordered β" consisting of sub-β" and disordered regions form at peak-aging.•Disordered β" evolve to β"/β'/B′/U2 composite precipitates at over-aging.•The composite precipitates are responsible for enhanced alloy thermal stability. Display omitted The Al-Mg-Si alloys added with trace Sc demonstrates an improved thermal stability, as compared with that without Sc-addition. But the microstructural origin of the enhanced property is unclear. In the present study, the precipitates formed in an Al-Mg-Si-Sc alloy were studied in detail by atomic-resolution scanning transmission electron microscopy. It is shown that the dominant precipitates formed at the peak-aging condition are the disordered β" precipitates consisting of Sc-free β" sub-units and Sc-containing disordered regions, rather than the well-ordered β". Upon further aging, these disordered β" precipitates will evolve to β"/β'/B′/U2 composite precipitates. The formation of the composite precipitates is probably associated with the strong binding between Sc and Si atoms, and with the non-preference for Sc atoms to occupy the atomic sites of the β"-structure. Our study reveals the following: It is the formation of stabilized β"-related composite precipitates that enhances the thermal stability of the Sc-added Al-Mg-Si alloy.