Crop residue incorporation is considered as a promising approach for improving carbon sequestration coupling with soil aggregation (MWD). However, better understanding is needed regarding to the mechanism of carbon sequestration and aggregation following crop residue return in subtropical clay soil. A short-term field experiment (1.5 years) was conducted to explore the underlaying potential mechanism of carbon sequestration after crop residues return in the subtropical clay soil. Four treatments were applied as follows: (1) Control, (2) Inorganic fertilization (NPK), (3) Crop residue at 8-ton ha−1, (6) NPK + Crop residue at 8-ton ha−1. MWD, soil organic carbon (SOC), microbial biomass carbon (MBC), glomalin protein (GRSP), mineral and aggregate-associated SOC, and Fe oxides were determined. Results exhibited that the mineral nutrients with or without crop residue enhanced the SOC significantly in comparison to the only straw and control treatments (P < 0.05). The short-term residue return enhanced the MWD compared to the baseline soil, which was less than control due to the greater concentration of amorphous Fe oxides. Moreover, GRSP and MBC were significantly increased upon crop residue return in presence of mineral nutrients treatment (P < 0.01). SOC was reduced in the order of NPK > NPK + Crop residue > Crop residue > control, while MBC and GRSP were increased in the order of control < Crop residue < NPK < Crop residue + NPK. Aggregate-associated and mineral-associated SOC of aggregates were enhanced in presence of mineral nutrients (P < 0.001). Our results suggest that the nutrients addition in presence or absence of crop residue return under short-term field experiment is considered as a promising and sustainable clay soil management approach for enhancing carbon sequestration to mitigate climate change.