The North China Plain is an important summer maize/winter wheat rotation area. However, over the years, continued intensive tillage has destroyed the soil aggregate accelerating the mineralization and decomposition of soil organic carbon (SOC), which plays an important role in soil quality, as increased organic carbon storage improves soil fertility and crop yields. Thus, the objective of this study was to explore the comprehensive impact of tillage methods on soil aggregates, aggregate-associated SOC, and carbon sequestration capacity under a regime of straw return. In 2002, we started a 14-year long-term tillage experiment; then in 2016–2017, we tested the following tillage methods, zero tillage (ZT), rotary tillage (RT), subsoiling (SS), and conventional tillage (CT). The results showed that in the 0–10 cm soil layer, tillage methods significantly reduced the proportion of aggregates in the order of 2–0.25 > 5–2 > 0.25–0.053 mm. Additionally, conservation tillage (i.e., SS and ZT) significantly increased the percentage of macroaggregates (0–40 cm) and their SOC content, compared to CT. Additionally, the contribution rate of macroaggregates to SOC was 17.2% and 30.6% higher under SS and ZT than under CT, respectively. Conservation tillage methods improved the carbon sequestration capacity of soil aggregates. Our study provides a theoretical basis for the development of more suitable tillage methods. Furthermore, long-term conservation tillage seemingly protected large aggregates and, SOC, whereby carbon sequestration was enhanced and soil carbon emissions were effectively reduced.