To understand the degradation mechanism of the copper-ion-exchanged SSZ-13 (Cu-SSZ-13) is of high significance for rationally designing a zeolitic catalyst for ammonia-selective catalytic reduction of NOx (NH3-SCR). In this work, we focused on an Al-rich Cu-SSZ-13 and studied its structural degradation under hydrothermal conditions through a set of characterization techniques, including in situ X-ray diffraction (XRD), pair distribution function analysis and transmission electron microscopy–energy dispersive X-ray analysis (TEM–EDX). The results indicated that the chabazite structure tends to contract in the c direction upon hydrothermal treatment and consequently leads to the collapse of the four-membered ring. Such a structure change then results in the movement of isolated Cu2+ species from the face of the double six-membered ring to its center, which damages the structure further. However, the larger rings (6MRs and 8MRs) partially remain during the structure degradation, which possibly explains that some of the isolated Cu2+ species are alive even when the XRD-detectable crystallinity completely loses. The particle-by-particle observations through TEM–EDX analysis suggested that the occurrence of structural degradation differs remarkably from one individual particle to another. In general, particles with smaller size, having a lower Si/Al ratio and a higher Cu/Al ratio, tend to degrade easily. These results offer a thorough understanding of the structural degradation of Cu-SSZ-13 from the microscopic point of view and point out that the uniformity in composition and particle size of the zeolites plays a critical role in the early-stage degradation.