As the basic units of soil structure, soil aggregate are essential for maintaining soil stability. Intensified freeze-thaw cycles have deeply affected the size distribution and stability of aggregate under global warming. To date, we are still lacking about the effect of freeze-thaw cycles on aggregate in the permafrost regions of the Qinghai-Tibetan Plateau (QTP). Therefore, we investigated the effects of diurnal freeze-thaw cycles and seasonal freeze-thaw processes on soil aggregate by in-situ studies. Our results showed that the durations of thawing and freezing periods in the 0-10 cm soil layer were longer than in the 10-20 cm soil layer, while the opposite for 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 might not have significant effect on the size distribution and stability of aggregate. However, < 0.25 mm fraction dominated wet sieving aggregate with the highest proportion during the thawing period, while the proportions of 0.5-1 mm and 1-3 mm fractions reached the highest during the completely frozen period in the 0-20 cm layer (P < 0.05). Likewise, the mean weight diameter and water-stable aggregate were decreased during the thawing period compared with 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 a scientific guidance for evaluating the effects of freeze-thaw cycles on aggregate and provides a theoretical basis for further exploration on soil and water conservation in the permafrost regions of the QTP.