Soil cracking induced by grassland degradation has become increasingly common in the Qinghai‐Tibetan Plateau in recent decades, and the intensification of soil cracking has implications for soil carbon (C) cycling. However, how patchy degradation affects soil aggregates and organic C and the underlying mechanisms remain unclear. In the present study, we investigated the changes in soil aggregates and organic C across various degradation stages in patchy alpine swamp meadows. The results showed a hump‐shaped trend in the proportion of macroaggregates, mean weight diameter (MWD), macroaggregate‐associated organic C (MAOC), and their contribution to soil organic carbon (SOC) throughout the degradation sequence. Conversely, the proportion of microaggregates initially decreased and then increased, with the contribution of microaggregate‐associated organic C (MIOC) to SOC increasing as degradation progressed. Regression and piecewise structural equation modeling (SEM) showed that soil texture played a decisive role in the change in MAOC and MIOC, and enzyme activity was the key factor leading to the difference between MAOC and MIOC. Enhanced enzyme activity accelerated the decomposition of MAOC while favoring the accumulation of MIOC. These findings are crucial for understanding the mechanisms influencing the physical protection of SOC by aggregates under patchy degradation. This emphasized soil cracking as a turning point in aggregate and organic C changes and a trigger for severe degradation in alpine swamp meadows, warranting proactive measures to mitigate its onset and progression.