The appropriate combined nitrogen and phosphorus fertilization strategy is essential for obtaining higher grain yields while maintaining soil fertility. Here, a long-term split-plot design farmland experiment with five N fertilizer rates combined with four P fertilizer rates was established during 2016–2019 to determine an appropriate nitrate-N threshold in intensive managed winter wheat- summer maize cropping, and then propose the fertilization strategy based on NO3-N threshold to balances crop yield and soil nitrogen supply capacity. The results showed that N fertilizer increased accumulated NO3-N, while the combined phosphate fertilizer at each N rate reduced the accumulated NO3-N to different degrees. With the increasing of planting seasons, the residual soil NO3-N reached a steady-state balance of soil N pool when N application rate was 150–225 kg ha−1 combined 60–120 kg ha−1 P rate. The residual NO3-N threshold was determined as 100 kg ha−1 to maintain N supply capacity and prevent it leaching. Based on it, we recommend 154 kg ha−1 of N and 106 kg ha−1 of P fertilizer in the wheat season, and 162 kg ha−1 of N and 122 kg ha−1 of P fertilizer in the maize season. The optimized fertilizer strategy reduced the fertilizer by 67 kg N ha−1 per year and reduced the residual NO3-N by 34.2% in deep soil while only reducing average yield by 3.1% across crops and years. This study can serve as basis for sustainable solutions for balances grain yields and soil nitrogen supply capacity as well as preventing nitrate pollution in farmland.