Abstract: The North China Plain is a major grain production area in China, and wheat-maize rotation is the main cropping pattern in this region. Long-term straw returning and shallow rotary tillage have caused soil quality problems, such as a shallow plow soil layer, thickening of the plow bottom, and nutrient accumulation at the soil surface. These problems restrict a sustainable and stable grain yield. This study examined the effects of different agricultural management practices of tillage measures and methods of straw returning of physical protection on the soil aggregate composition and stability, the distribution of organic carbon and nitrogen in the aggregates at the Luancheng Agricultural Ecosystem Experimental Station, Chinese Academy of Sciences. A tillage and straw counters-field positioning experiment was conducted from 2016 with five treatments: no-straw and rotary tillage (as control 1, RT), straw mulching and rotary tillage (as control 2, SR), straw mulching and deep ploughing (SP), straw incorporated into 0−40 cm soil layer of 40 wild no-wheat planting belt (SID), and straw buried into 30−40 cm soil layer (SBD). The three latter treatments represented different straw returning methods. The results showed that changing rotary tillage to deep tillage under straw returning significantly increased the content of large macroaggregates (>0.25 mm). Different straw returning methods led to significantly different changes in water stability of the large (>2 mm) and small (0.25–2 mm) macroaggregates. Straw returning to the deep soil layer increased the content of large water-stable macroaggregates in soil layers below 10 cm (>2 mm), whereas increased the content of small water-stable macroaggregates (0.25–2 mm) in the surface layer. The changes in the water stability of large and small macroaggregates were impacted by the straw returning method. Straw returning to deep soil layer significantly increased the stability in the subsurface layer (20–40 cm) and decreased the structural fragmentation rate of soil aggregates. Deep straw returning effectively integrated the 0–40 cm soil layer, eliminated the surface accumulation of nutrients, and significantly increased the soil organic carbon and nitrogen contents in the subsurface layer and the contribution of large macroaggregates to soil organic carbon and nitrogen. The contribution of organic carbon and nitrogen of the macroaggregates (>2 mm) in the 20–40 cm soil layer was 42.2%–44.0% and 32.8%–49.9%, respectively, which increased by 48.7%–54.9% and 32.8%–101.8%, respectively, compared to straw-free rotary tillage. In summary, the straw returning to deep soil layer improved soil structure of tillage layer, promoted integration of soil layers and emilimated nutrient accumulation in soil surface layer.