As the basic units of soil structure, soil aggregate is essential for maintaining soil stability. Intensified freeze–thaw cycles have deeply affected the size distribution and stability of aggregate under global warming. To date, it is still lacking about the effects of freeze–thaw cycles on aggregate in the permafrost regions of the Qinghai-Tibetan Plateau (QTP). Therefore, we investigated the effects of diurnal and seasonal freeze–thaw processes on soil aggregate. Our results showed that the durations of thawing and freezing periods in the 0–10 cm layer were longer than in the 10–20 cm layer, while the opposite results were observed during completely thawed and frozen periods. Freeze–thaw strength was greater in the 0–10 cm layer than that in the 10–20 cm layer. The diurnal freeze–thaw cycles have no significant effect on the size distribution and stability of aggregate. However, < 0.25 mm fraction dominated wet sieving aggregate with the highest proportion during thawing period, while the < 1 mm fraction reached the highest during completely frozen period in the 10–20 cm layer ( P < 0.05). Likewise, the mean weight diameter and water-stable aggregate were decreased during thawing period compared with the other periods, which were influenced by soil microbial biomass carbon and belowground biomass. Hence, the seasonal freeze–thaw processes destroyed macro-aggregate (> 0.25 mm) and reduced aggregate stability. Our study has scientific guidance for evaluating the effects of freeze–thaw cycles on soil steucture and provides a theoretical basis for further exploration on soil and water conservation in the permafrost regions of the QTP.