Integrated agronomic optimization (IAO) adopts suitable crop varieties, sowing dates, planting density and advanced nutrient management to redesign the entire production system according to the local environment, which can achieve synergistic improvements in crop yields and resource utilization. However, the intensity and magnitude of the impacts of IAO on soil quality under long-term intensive production and high nitrogen use efficiency (NUE) require further clarification. Based on a 13-year field experiment conducted in Dawenkou, Tai'an, China, we investigated the effects of four cultivation modes on the grain yield, NUE, soil aggregate structure, as well as the fraction of organic matter (SOM) and soil quality, reflected by integrated fertility index (IFI) during the winter wheat maturation period in 2020–2022. The four cultivation modes were traditional local farming (T1), farmer-based improvement (T2), increased yield regardless of production cost (T3), and integrated soil–crop system management (T4). As IAO modes, T2 and T4 were characterized by denser planting, reduced nitrogen (N) fertilizer application rates, and delayed sowing compared to T1 and T3, respectively. In this long-term experiment, IAO was found to maintain aggregate stability, increase SOM content (by increasing organic carbon and total nitrogen of the light fraction (LF) and the particulate organic matter fraction (POM)), and improve SOM quality by increasing the proportions of LF and POM and the ratio of organic carbon to total nitrogen in SOM. Compared to T1, the IFI of T2, T3, and T4 increased by 10.91, 23.38, 25.55%, and by 17.78, 6.41, 28.94% in the 0–20 and 20–40 cm soil layers, respectively. The grain yield of T4 was 22.52% higher than that of T1, reaching 95.98% of that in T3. Furthermore, NUE of T4 was 35.61% higher than that of T1 and T3. In conclusion, our results suggest that T4 synergistically increases grain yield and NUE in winter wheat, while maximizing soil quality.
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