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In agricultural ecosystems, one optimized crop residue management practice, i.e., incorporating biochar produced from crop residues via pyrolysis to the soil, is considered a promising technology for mitigating climate change and improving soil quality. However, the potential mechanisms are still not well known. In this study, a five-year (2011-2015) field experiment in a Mollisol of Northeast China that included four treatments, i.e., CK (no fertilizer), NPK (mineral nitrogen, phosphorus and potassium fertilizers), NPKS (NPK plus maize straw) and NPKB (NPK plus maize straw-derived biochar), was conducted to evaluate the effects of maize straw and its derived biochar application on the following: 1) the size distribution and water stability of soil aggregates; 2) the concentrations of organic and humic carbon (C) in bulk soil and water-stable aggregate fractions; and 3) the chemical compositions of organic and humic C in water-stable aggregate fractions. Compared with the CK and NPK treatments, the proportion of macroaggregates (> 0.25 mm) [mainly large macroaggregates (> 2 mm)] increased whereas the proportions of microaggregates (0.25-0.053 mm) and silt + clay fractions (< 0.053 mm) decreased in NPKS and NPKB treatments, resulting in the mean weight diameter (MWD) of soil aggregates being higher under NPKS and NPKB treatments than under CK and NPK treatments. The concentrations of organic and humic C in bulk soil and aggregate fractions were also generally higher under NPKS and NPKB treatments than under CK and NPK treatments. The treatment effects were more apparent for NPKB than for NPKS. With respect to other treatments, the NPKB treatment significantly increased the ratios of macroaggregate- to microaggregate-associated organic C as well as humin C. The solid-state C-13 cross-polarization magic-angle-spinning (CPMAS) NMR spectra of small macroaggregates (2-0.25 mm) and its humic acid fraction showed that the NPKS treatment did not alter the proportions of the C functional groups. In contrast, the NPKB treatment clearly decreased the proportions of alkyl C and O-alkyl C but increased the proportion of aromatic C, resulting in the alkyl C/O-alkyl C and hydrophobic C/hydrophilic C ratios being higher whereas the aliphatic C/aromatic C ratio was lower under NPKB than under other treatments. These findings indicate that the application of maize straw biochar enhanced soil aggregate stability and aggregate-associated organic and humic C concentrations. Biochar C was preferentially incorporated into macroaggregates and its humin fraction with respect to microaggregates. Moreover, the molecular structure of small macroaggregates and its HA fraction became more stable, hydrophobic and aromatic. Therefore, physical protection through organic C in aggregate fractions, physical-chemical protection through the encapsulation of humic C within aggregate fractions, and physical-biochemical protection through recalcitrant alkyl C and aromatic C within aggregate fractions may be the primary mechanisms for C preservation in biochar-amended soil. Our results suggested that maize straw biochar application was an effective strategy based on the comprehensive goal of mitigating climate change and improving soil quality in Mollisols of Northeast China.