Improving soil quality while maintaining agricultural productivity is a key challenge in sustainable agriculture. Diversified cropping systems offer a promising approach, but their impacts on soil quality via aggregates and carbon sequestration need further investigation. This study investigated the effects of peanut-based rotations—winter fallow–spring peanut (CP), winter wheat–summer peanut (WP), winter wheat–summer maize→winter fallow–spring peanut (WMP), and winter wheat–summer maize→winter wheat–summer peanut (WMWP)—on soil aggregates and carbon sequestration, compared to conventional winter wheat–summer maize rotation (WM) in Huang-Huai-Hai Plain of China. Results show that, WP, WMP, and WMWP rotations significantly improved mean weight diameter (24.89–47.29%) and geometric mean diameter (20.35–34.38%) in the 0–20 cm soil layer, compared to CP and WM. These rotations also enhanced carbon sequestration, with small macroaggregates contributing 51–59% of total bulk soil carbon. WMWP rotation notably increased particulate organic carbon (POC) and recalcitrant organic carbon, leading to significant increases in total organic carbon (+14.91%), soil organic carbon storage (+19.97%), and the carbon pool management index (+53.09%) compared to WM. Overall, peanut-based rotations (WP, WMP, and WMWP) improved the soil quality index by 37.47–211.66% compared to WM, driven by increased aggregate stability and carbon sequestration. This study highlights the critical role of small macroaggregates in soil organic carbon retention and the potential of peanut-based rotations in sustainable agriculture.