The competition mechanisms between crop species for water and nutrients, especially nitrate (NO3-N), in intercropping ecosystems are still poorly understood. Therefore, an experiment involving high (300 kg ha-1 for corn and 250 kg ha-1 for tomato), medium (210 kg ha-1 for corn and 175 kg ha-1 for tomato), and low (150 kg ha-1 for corn and 125 kg ha-1 for tomato) N-fertilizer applications (HF, MF, LF, respectively) was conducted in the corn and tomato intercropping ecosystem during 2014 (a calibration period for modeling) and 2015 (a validation period for modeling). The modified HYDRUS-2D code was used to analyze soil NO3-N concentrations (SNC) in the middle between corn rows (Pc), between corn and tomato rows (Pb), and between tomato rows (Pt), NO3-N exchange in the horizontal direction between different regions, NO3-N leaching from the corn, the bare, and the tomato region, and N uptake by crops. Simulated SNCs were in good agreement with measurements, with RMSE, NSE, and MRE of 0.01-0.06 mg cm-3, 0.75-0.98, and 8.7-19.1%, respectively, during the validation period (2015). Average SNCs in the 0-40 cm soil layer were different between Pc, Pt, and Pb. Intensive NO3-N exchange in the horizontal direction occurred during the second stage (Day After Sowing [DAS] 37-113 in 2014; DAS 29-120 in 2015). NO3-N exchange between the corn and bare regions was lower than between the tomato and bare regions due to smaller concentration gradients. However, in the vertical direction, NO3-N leaching from the corn region in both years was 4.1 and 8.8 times larger, respectively, than from the tomato region under HF since NO3-N mainly moved from the tomato region to the corn region. Our results reveal the competition between corn and tomato for N and provide a rationale for formulating and optimizing different fertilizer regimes for different crops in the intercropping ecosystem.