Context or problemLone-term application of chemical fertilizers in farmland ensure adequate or profitable crop yields but may damage soil structure. Cover crops (CCs) have great potentials to improve soil quality and promote sustainable crop production. However, the combined impacts of CCs with nitrogen fertilization on soil quality and crop yields are not clear. Objective or research questionWe aimed to examine the effects of CCs combined with N fertilization rates on soil physical properties, C and N fractions in both bulk soils and aggregates, and crop yields, and to find the best management practice that improve both soil quality and crop yields synthetically. MethodsA 4-year summer CCs - winter wheat field experiment was conducted in the Loess Plateau of China. CCs with different species and combinations (CC) were soybean (SB), sudan grass (SG), a mixture of both (SS), and no cover crop (CK) and N fertilizer (NR) were applied to winter wheat at rates of 0 (N0), 60 (N60), and 120 (N120) kg N ha−1. Soil physical properties and C and N fractions in both bulk soils and aggregates were evaluated at 0–10, 10–20, and 20–40 cm soil depths. ResultsSoil total porosity (TP), saturated water content (SWC), capillary water capacity (CWC), and C and N fractions decreased while bulk density (BD) increased with the increase of soil depth. The CC, NR, and their interaction (CC×NR) had significant effects on soil BD, aggregate size distribution and stability (MWD), and C and N fractions and only CC and CC×NR had significant effects on other physical properties. The incorporation of CCs significantly increased the proportions of > 5 mm aggregates and C and N fractions in both bulk soils and aggregates, especially in 0–10 and 10–20 cm. And SB and SS improved soil other physical properties more than SG, especially in 0–10 cm, which decreased BD by 13.2% and 12.6% while increased TP by 6.5% and 8.3%, SWC by 14.3% and 15.3%, CWC by 13.9% and 14.2%, MWD by 16.6% and 14.4%, respectively, compared to CK. Additionally, soil physical properties improved more with N60 while the C and N fractions in both bulk soils and aggregates increased more with N120. However, BD increased by 2.6% and 3.3% in N60 and N120 than N0, respectively. The correlations between the proportion of macro-aggregates and soil C and N fractions at 0–10 and 10–20 cm indicated the positive effects of CCs on improving soil structure and fertility simultaneously. Aggregated-associated C and N fractions decreased firstly and then increased with the reduced aggregate sizes, and were higher in micro-aggregates than in other size classes. N60-SB increased wheat yields by 98.7% compared with N0-CK. ConclusionsOverall, the incorporation of soybean residue was the best management practice for winter wheat yield and soil fertility under the reduced N fertilization. Implications or significanceThe selection of CCs species should depend on farmland managements, and the appropriate CCs with N fertilizer rates would target the improvements in soil quality, the sequestration of soil organic carbon, and crop yields synergistically.