A synchronous increase in crop productivity, nutrient use efficiency, and soil carbon(C) sequestration is important from the point of view of food security and environmental protection. In recent years, integrated soil-crop system management(ISSM), which uses crop models and advanced nutrient management to redesign cropping systems, has been successfully demonstrated to achieve both high crop productivity and high nutrient use efficiency in China, but the effects of ISSM on soil organic C(SOC) characteristics remain unknown. In this study, the effects of current farmers’ practice(FP), high-yielding practice(HY), which maximizes yields without considering costs, and ISSM on the content and chemical composition of SOC were studied in a 4-year(2009–2013) field plot experiment with maize(Zea mays L.) monoculture in an Alluvic Primosol in Northeast China. The ISSM resulted in higher soil total organic C(TOC), water-soluble organic C, easily-oxidizable organic C, particulate organic C, and humic acid C compared with HY and FP in the region. The SOC contents in aggregate size fractions generally followed a similar pattern to TOC. Compared with FP,HY decreased the mean weight diameter, geometric mean diameter, percentage of > 0.25-mm water-stable aggregates, and the stability ratio of water-stable aggregates, and increased the structure-deterioration rate and index of unstable aggregates. The opposite trend was observed between ISSM and HY. Solid-state ~(13)C nuclear magnetic resonance spectra of bulk soil showed that ISSM had higher O-alkyl C and aliphatic C/aromatic C ratio, but lower aromatic C, carbonyl C, and alkyl C/O-alkyl C and hydrophobic C/hydrophilic C ratios than HY and FP. Our results suggest that ISSM improves the quantity and quality of SOC and has a positive effect on soil aggregation and aggregate stability. A synchronous increase in crop productivity, nutrient use efficiency, and soil carbon (C) sequestration is important from the point of view of food security and environmental protection. In recent years, integrated soil-crop system management (ISSM), which uses crop models and advanced nutrient management to redesign cropping systems, has been successfully demonstrated to achieve both high crop productivity and high nutrient use efficiency in China, but the effects of ISSM on soil organic C (SOC) characteristics remain unknown. In this study, the effects of current farmers’ practice (FP), high-yielding practice (HY), which maximizes yields without considering costs, and ISSM on the content and chemical composition of SOC were studied in a 4-year (2009-2013) field plot experiment with maize (Zea mays L.) monoculture in an Alluvic Primosol in Northeast China. The ISSM resulted in higher soil total organic C (TOC), water-soluble organic C, easily-oxidizable organic C, particulate organic C, and Compared with HY and FP in the region. The SOC contents in aggregate size fractions generally followed by a similar pattern to TOC. Compared with FP, HY decreased the mean weight diameter, geometric mean diameter, percentage of> 0.25-mm water- stable aggregates, and the stability ratio of water-stable aggregates, and increased the structure-deterioration rate and index of unstable aggregates. The opposite trend was observed between ISSM and HY. Solid-state ~ (13) C nuclear magnetic resonance spectra of bulk soil showed that ISSM had higher O-alkyl C and aliphatic C / aromatic C ratio, but lower aromatic C, carbonyl C, and alkyl C / O-alkyl C and hydrophobic C / hydrophilic C ratios than HY and FP. Our results suggest that ISSM improves the quantity and quality of SOC and has a positive effect on soil aggregation and aggregate stability.