Aggregate has been recognized as a key element in the stabilization of soil organic carbon (SOC). Several researchers have done outstanding work on identifying and isolating aggregates and their physiochemical properties. However, thermal stability of SOC in soil aggregates has not yet been adequately explored. The main objective of the study was to clarify the protection of aggregation on SOC from thermal characters, and provide evidence on whether thermal analysis could be a potential rapid method to determine SOC stability in aggregates. We separated 20-cm surface soil into six fractions (>2, 1-2, 0.5-1, 0.25-0.5, 0.053-0.25 and <0.053mm) before and after 23-yr continuous soybean cultivation. The study measured the change of SOC and its thermal characteristics across aggregates using thermogravimetry-differential scanning calorimetry (TG-DSC), which also showed that the thermal stability mechanism of SOC is protected by aggregates. Results showed that 23-yr continuous soybean cultivation led to an SOC increase in 0.053-0.5 mm size aggregates, but a decrease in other large-size aggregates. Energy density in the > 0.5 mm fraction was decreased by 23-yr continuous soybean cultivation, but increased to < 0.5 mm size fraction. The largest energy density was in < 0.053 mm size fractions. In conclusion, long-term continuous soybean cultivation led to more energy transferred to micro-aggregates associated with the protection of micro-aggregates on soil SOC.