Crop residue is a commonly used organic soil amendment in summer maize (June–October)–winter wheat (October–June of next year) rotation systems. However, the effects of different straw return modes on soil aggregation and soil organic carbon (SOC) stocks in different water-stable aggregates have not been extensively investigated in these cropping systems. The objective of this study was to quantify the long-term (7 yr) impact of C input on the SOC content of four soil aggregate size classes (large macroaggregates; small macroaggregates; microaggregates, silt plus clay fraction) and in explicit SOC fractions (free light fraction, free LF; intra-aggregate particulate organic matter, iPOM; mineral-associated matter, mSOM) within the top 40cm of soil in a wheat–maize double cropping system in Northwest China. Four treatments were examined: (i) no return (control); (ii) return of wheat straw only (WR); (iii) return of maize straw only (MR); and (iV) return of both maize and wheat straw (MR-WR). Over the experimental period, the change in SOC under the four treatments ranged from −0.96 to 5.83Mgha−1 and a significant linear relationship between SOC change and cumulative C input (R2=0.9882, P<0.05) was observed. Relative to the control, the proportion of large and small macroaggregates in the 0–20cm soil layer increased the most in MR-WR (32% and 24%), followed by MR (22% and 13%), and WR (11% and 10%). Straw return significantly increased the SOC content in each soil aggregate size class relative to no straw return. The order of SOC fractions with respect to SOC content was mSOM>fine iPOM>coarse iPOM>free LF. Straw return significantly increased the C stock in iPOM and mSOM relative to the control. Coarse iPOM was the most sensitive indicator of C change and mSOM was the main form of SOC under long-term straw return. A significant linear relationship existed between cumulative C input and the mass proportion of macroaggregates as well as the C content of SOC fractions (or aggregate fractions). Soil depth had a significant influence on almost all measurements, with greater values observed in the 0–20cm layer than in the 20–40cm layer. Overall, return of both maize and wheat straw was the best strategy for improving soil structure, soil organic carbon, and crop yield. However, straw return from one crop was sufficient to maintain initial SOC levels, and conserved straw could be used for cellulosic feedstocks.