How different fertilization practices modify soil organic carbon (SOC) sequestration is still unclear. Our study aimed to evaluate the changes in SOC stocks and their physical fractions after 10 years of organic and inorganic fertilization. Five treatments were established under a wheat-maize system in Northern China: control (CK), chemical fertilizer (F), straw plus chemical fertilizer (SF), manure plus chemical fertilizer (MF), and straw and manure plus chemical fertilizer (SMF). The results showed that the SOC sequestration rate at 0–20 cm depth decreased in the following order: SMF (1.36 Mg C/ha/yr) > MF (1.13 Mg C/ha/yr) > SF (0.72 C/ha/yr) > F (0.15 Mg C/ha/yr) > CK (−0.25 Mg C/ha/yr). The values indicated that straw returning and manure application were important measures to achieve the “4 per 1000” target, and the application of manure was a more effective strategy. The high input of chemical fertilizer only maintained the initial SOC level and was not a powerful C-farming practice. A minimum input of 4.93 Mg C/ha/yr was required to keep the initial SOC storage. The SOC associated with small macroaggregate (0.25–2 mm) was the most sensitive indicator for the changes of bulk SOC. In addition, the accumulation of SOC under SMF, MF, and SF treatments mainly occurred in the occluded particulate organic C (oPOC) in small macroaggregates, indicating that the physical protection of macroaggregates played a predominant role in SOC sequestration. The SMF, MF, and SF treatments also displayed higher mineral organic C (mSOC) in soil aggregates than the CK and F treatments. A transformation of oPOC towards the mSOC fraction indicated that exogenous C further shifted into stable C pools under the physical protection of soil aggregates. In conclusion, these findings confirmed the important role of straw returning and manure application in SOC accumulation and stabilization, highlighting that a combination strategy of straw + manure + chemical fertilizer had the best effect.