Cereal can stimulate legume N fixation through competition for soil mineral N. In addition, organic acids in the rhizosphere can mobilize external nutrients, which may help nodulation. However, how much NO3− and NH4+ competition and organic acids in the rhizosphere of intercropped crops contribute to N fixation remains unclear and requires study. Field and greenhouse experiments were conducted to quantify effects of N competition and organic acids on N fixation in a maize/alfalfa intercropping system. Intercropping increased nitrogen derived from the atmosphere (%Ndfa), nodules number, and leghemoglobin content by 43.66%, 85.53%, 141.05%, respectively, leading to significantly improved total N uptake and yield, compared to monoculture. The improved %Ndfa was not only due to the depletion of NO3−, but also significantly correlated with the decrease of NO3−/NH4+ ratio and the increase of citric acid in rhizosphere of alfalfa, which could mobilize soluble resources for N fixation under no N addition. Overall, 15.4%–21.5% of N fixed by alfalfa was transferred to associated maize, and the improved N fixation enhanced N transfer. Our findings provide a mechanism for how root interactions facilitate N fixation, highlighting the importance of NO3−/NH4+ ratio and citric acid in nutrient mobilization for N fixation.