<p>Climate change and nitrogen (N) application significantly influence agricultural productivity and soil greenhouse gas emissions. However, the interactive effects of interannual climate variability and N fertilization legacy on corn yield and soil nitrous oxide (N₂O) emissions remain inadequately understood. In this study, we employed the DeNitrification-DeComposition (DNDC) model to simulate corn yield and soil N₂O emissions over a 40-year period (1981–2020). We designed a series of experiments by adjusting climate year data to quantify interannual variability in corn yield and soil N₂O emissions, while also disentangling the contributions of climate variability and N legacy effects. The results revealed substantial interannual variability in both corn yield and soil N₂O emissions. Corn yield was primarily driven by changes in growing season precipitation, while soil N₂O emissions were influenced by precipitation, exchangeable ammonium N (NH₄⁺), and nitrification-denitrification processes. Severe drought strongly reduced corn yield, while soil N₂O emissions exhibited a gradual yet pronounced legacy effect of N application, increasing from 1.69 to 7.85 kg N·ha⁻¹ over the 40-year period. This study highlights the relatively weak influence of interannual climate variability compared to the stronger legacy effects of N application on crop yield and soil N₂O emissions, providing valuable insights for sustainable agricultural and environmental management.</p>