Using fractionation of aggregate and occluded microaggregate techniques, the present study was performed to determine the organic carbon (C) content in aggregates and subfractions within aggregates of three ecosystems, including the grassland, farmland, and bare land in a long-term (27-year) trial in typical Mollisols of Northeast China. We aimed to analyze the links between aggregation and aggregate-protected C, and to reveal the physical protection mechanism of organic C stabilization of Mollisols. We found that, as compared with the farmland, the grassland showed significantly increased soil organic C (SOC) content by 7.6%; in contrast, the bare land showed greatly decreased SOC content by 14.1%. The grassland promoted the formation of macroaggregates (> 250 μm), especially the large macroaggregates (> 2000 μm), and significantly increased the mean weight diameters (MWD) of aggregates and thus aggregate stability. However, the proportions of macroaggregates and microaggregates decreased, while the proportion of silt and clay particles increased accordingly in the bare land, indicating a deaggregation effect. As compared with the farmland, the C contents in microaggregates and silt and clay particles decreased, but increased the C contents in macroaggregates and all subfractions within macroaggregates in the grassland. Compared with the farmland, the C contents in coarse particulate organic matter (cPOM_M), occluded microaggregates (mM), and silt and clay particles (S&C_M) in the grassland increased by 600%, 54% and 65%, respectively. In the bare land, the C contents increased in silt and clay particles, but decreased in macroaggregates, microaggregates, and in all subfractions within them. Carbon associated with silt and clay particles as passive C pool represents a major part of the total C stock of Mollisols of the three ecosystems, which accounted for 52%-79% of the total SOC. The accumulation or loss of Mollisols in Northeast China was mainly due to the intra-aggregate particulate organic matter (iPOM) fraction as relatively active C pool. The increment of organic C in the grassland relative to the farmland was primarily located in total coarse particulate matter (total cPOM) in macroaggregates, which was three times of the total increases in bulk SOC in the grassland as compared with that of the farmland. The loss of organic C in the bare land relative to the farmland was primarily located in total fine particulate matter (total fPOM) in microaggregates, which contributed to 60% of the total loss in bulk SOC in the bare land relative to the farmland.