Soil aggregate stability and pore structure are key indicators of soil degradation. Waves generated by the water-level fluctuations could severely deteriorate soil aggregates, which eventually induce soil erosion and several other environmental issues such as sedimentation and flooding. However, due to limited availability of the hydrological alteration data, there is a limited understanding of soil aggregates, intra-aggregate pore dynamics, and their relationships under periodically flooded soils. The present study has relied on long-term hydrological alteration data (2006-2020) to explore the impacts of inundation and exposure on soil aggregates and pore structure variations. Soil samples from increasing elevations (155, 160, 163, 166, 169, and 172 m) in the water-level fluctuation zone of the Three Gorges Reservoir were exposed to wet-shaking stress and determined soil structural parameters. The overall inundation and exposure ratio (OvI/E) gradually decreased from 1.87 in the lowest to 0.27 in the highest elevation, respectively. Predominant distribution of macropores was recorded in lower elevations, while micropores were widely distributed in the upper elevations. The mean weight diameter (MWD) was significantly lower in the lower (2.4-3.7 mm) compared to upper (5.3-6.0 mm) elevations. The increase in MWD has increased the proportion of micropores (PoN < 50 mu m), with R-2 = 0.59. This could suggest that the decrease in flooding intensity can create favorable conditions for plant roots growth. The strong flooding stress in lower elevations (i.e., higher values of the OvI/E) accelerated the disintegration of soil aggregates and considerably increased the formation of macropores due to slaking and cracking. The findings of the present study emphasize the need to restore degraded soils in periodically submerged environments by implementing vegetation restoration measures. This could enhance and sustain aggregate stability, which was also proved to increase functional pores under hydrological alterations.