Agricultural organic waste can enhance aggregate organic carbon stability, which is crucial for soil carbon sequestration in croplands. However, it is unclear how aggregate organic carbon stability changes with different nature-based nutrient management practices, especially with partial organic substitution. This study aimed to elucidate how different organic wastes (chicken manure, biochar, straw, and carbon-based materials from kitchen waste) influence aggregate organic carbon stability, including aggregate stability, the content of physically protected organic carbon, and the decomposability of aggregate carbon. The improvement of aggregate organic carbon stability was trialed in a 4-year field experiment with equivalent nitrogen and organic carbon input under nature-based nutrient management. The results showed that all nature-based nutrient management practices improved aggregate organic carbon stability compared to no nutrient addition. Biochar application dramatically improved aggregate organic carbon stability by 5.8% – 11.4% in aggregate stability, 83.9% – 152.4% in aggregate organic carbon, and 36.6% – 75.0% in aggregate recalcitrant carbon content. By comparison, straw returning showed the lowest improvement in aggregate organic carbon stability, owing to substantial increases of microbial respiration and enzyme activities involved in carbon degradation. Organic carbon merely increased by 32.3%, 33.6%, and 29.5% in large macroaggregates, small macroaggregates, and microaggregates, respectively. This study dissected the different efficiencies of nature-based nutrient management in improving aggregate organic carbon stability in vegetable fields. The findings highlight that appropriate nature-based nutrient management with organic waste could better implement the carbon neutrality in agroecosystems from the perspective of aggregate organic carbon stability.