Partial substitution of chemical fertilizers with organic amendments represents a promising approach to sustainable soil management, yet its integrated effects on soil quality and elemental stoichiometry in Vertisols remain insufficiently understood. This study aimed to investigate the impacts of partial organic fertilizer substitution on soil quality, ecological stoichiometry, crop yield, and yield stability through a three-year, six-site field experiment in the North China Plain. Treatments included an unfertilized control, full chemical fertilization (NPK), and NPK partially substituted by pig manure at 15% and 30% of nitrogen input (15%M and 30%M). Results revealed that partial substitution significantly reduced soil bulk density (1.3–17.1%) and increased soil organic carbon (0.77–22.5%) compared with NPK and control plots. While total nitrogen (N), phosphorus (P), and potassium (K) contents were comparable to NPK, nutrient availability improved markedly (2.1–23.7%). Organic inputs also modified soil elemental stoichiometry by increasing C:N, C:P, and N:P ratios, indicating a shift toward more balanced nutrient states. These improvements translated into substantial increases in the Soil Quality Index (31.5–335.6%), which in turn supported significant yield gains in wheat and maize (1.3–251.3%), with the 30%M treatment consistently achieving the greatest benefits. Random forest analysis and structural equation modeling demonstrated that yield responses were predominantly mediated through improvements in soil quality, driven by enhanced nutrient availability and optimized stoichiometry. Overall, our findings suggest that partial substitution of chemical fertilizers with organic inputs-particularly at a 30% replacement rate-offers as an effective strategy to improve soil quality, mitigate nutrient imbalances, and promoting sustainable intensification of wheat–maize systems in Vertisol regions.

Introduction: Soil organic carbon (SOC) and total nitrogen (TN) stocks are key determinants of the productive capacity of agricultural soils. This study aims to elucidate the effects of long-term tillage practices combined with organic amendments on SOC and TN sequestration within soil aggregates and their subsequent relationship with wheat yield. Methods: A six-year field experiment (initiated in 2016) was conducted, evaluating the following treatments: rotary tillage with straw, rotary tillage with manure, rotary tillage with straw plus manure, deep tillage with straw, deep tillage with manure and deep tillage with straw plus manure. Results: Relative single organic amendments, both rotary and deep tillage with straw plus manure significantly enhanced macro-aggregate-associated SOC and TN stocks in the 0–15 cm layer by 7.86–23.29% and 16.36–18.99%, respectively. In the 15–30 cm layer, deep tillage with single organic amendments increased macro-aggregate-associated SOC and TN contents by 7.56–18.81% and 5.29–21.47%, respectively compared with rotary tillage. However, deep tillage also reduced macro-aggregate proportions by 5.36–8.16%, which decreased associated SOC and TN stocks by 6.12–7.87% and 6.99–8.53%, respectively. In contrast, deep tillage with straw plus manure increased macro-aggregate-associated SOC and TN contents (18.42–19.39% and 10.17–12.76%, respectively) without reducing macro-aggregate proportions, thereby enhancing SOC and TN stocks in macro-aggregates by 10.49–26.89% and 9.07–26.32%, respectively. Discussion: These findings indicate that the enrichment of subsoil macro-aggregate-associated SOC and TN strongly correlated with higher wheat yield, demonstrating that deep tillage with straw and manure is an effective practice for improving soil health and sustaining productivity.