Soil aggregation plays a critical role in the maintenance of soil structure and crop productivity. Fertilization influences soil aggregation, especially by regulating soil organic carbon (SOC) and total nitrogen (TN) contents in aggregate fractions. Here, we conducted a fixed-site field experiment to quantify the effect of five N application rates: 0, 75, 150, 225, and 300 kg·N·ha−1, denoted as N0, N75, N150, N225, and N300, respectively, on soil aggregate stability, aggregate-associated SOC and TN sequestration and crop productivity. Soil aggregates were divided into >0.25 (>5, 5–2, 2–1, 1–0.5, 0.5–0.25) and 0.25 mm), decreased the proportion of micro-aggregates (5 mm macro-aggregates in N225 was significantly increased by 19.24% under dry sieving (p p p p < 0.05). In conclusion, N225 was the suitable N application for improving soil aggregate stability, carbon and nitrogen sequestration, and crop productivity on the Loess Plateau, China.