An appropriate combined nitrogen (N) and phosphorus (P) fertilization strategy is essential for obtaining sustained higher grain yields while maintaining soil fertility. In this study, a long-term split-plot design farmland experiment (initiated in 2009) with five N fertilizer rates combined with four P fertilizer rates was established during 2016–2019 to determine an appropriate nitrate-N (NO3-N) threshold in an intensive managed wheat–maize double cropping system. A fertilization strategy was then proposed based on the NO3-N threshold to balance the crop yields and soil nitrogen supply capacity. The results showed that N fertilizer increased the accumulated NO3-N, and the combined application of phosphate fertilizer with each N rate reduced the accumulated NO3-N to different degrees. The residual soil NO3-N reached a steady-state soil N pool balance after long-term application of N at 150–225 kg ha−1 combined with P at 60–120 kg ha−1. The residual NO3-N threshold in the root zone (0–100 cm soil layer) was determined as about 100 kg ha−1 at the crop harvest to maintain the N supply capacity and prevent leaching into the deep soil (>100 cm soil layer). The fertilization guidelines are 154 kg ha−1 for N fertilizer and 106 kg ha−1 for P fertilizer in the winter wheat season, and 162 kg ha−1 for N fertilizer and 122 kg ha−1 for P fertilizer in the summer maize growing season based on the NO3-N safety threshold. The optimized fertilizer strategy reduced the fertilizer application rate by 67 kg N ha−1 per year and the residual NO3-N by 34.2% in the deep soil, while only reducing the average yield by 3.1% across the crops and years. These findings provide a basis for sustainably balancing grain yields and soil nitrogen supply capacity as well as preventing nitrate pollution of farmland.