Soil organic carbon (SOC) plays a key role in improving soil quality and optimizing crop yield.  Yet little is known about the fate of macroaggregates (>0.25 mm) under long-term fertilization and their relative importance in SOC sequestration in reclaimed calcareous soil.  Therefore, the effects of mineral fertilizers and organic manure on the mechanisms of organic carbon (OC) stabilization in macroaggregates were investigated in this study.  Four treatments were used: unfertilized control (CK), mineral fertilizer (NPK), compost chicken manure alone (M), and mineral fertilizers plus manure (MNPK).  Samples from the 0–20 cm layer of soil receiving 11-year-long fertilization were separated into four fractions based on the macroaggregates present (unprotected coarse and fine particulate organic matter, cPOM and fPOM; physically protected intra-microaggregate POM, iPOM; and biochemically protected mineral associated OM, MOM) by the physical fractionation method.  Compared with the control, the long-term application of NPK had little effect on SOC content, total nitrogen (TN) content, and OC and TN contents of macroaggregate fractions.  In contrast, incorporation of organic manure (MNPK) significantly increased SOC (45.7%) and TN (24.3%) contents.  Application of MNPK increased OC contents within macroaggregate-extracted fractions of cPOM (292.2%), fPOM (136.0%) and iPOM (124.0%), and TN contents within cPOM (607.1%), fPOM (242.5%) and iPOM (127.6%), but not the mineral associated organic carbon (MOM-C) and nitrogen (MOM-N) contents.  Unprotected C fractions were more strongly and positively correlated with SOC increase than protected C fractions, especially for cPOM-C, indicating that SOC sequestration mainly occurred via cPOM-C in the studied calcareous soil.  In conclusion, MNPK increased the quantity and stability of SOC by increasing the contents of cPOM-C and cPOM-N, suggesting that this management practice (MNPK) is an effective strategy to develop sustainable agriculture.