•  Long-term N and P application led to different nitrate residue levels.
  • Residual nitrate increased by N but decreased by combined P to different degrees.
  •  Suitable N and P application achieved steady-state soil N pool balance.
  • Residual NO3-N threshold in 0–100 cm soil layer determined as 100 kg ha−1.
  • Using threshold maintained soil N supply capacity and prevented NO3-N leaching.