Intercropping of cotton and legume plants offers long‐term crop productivity while saving agricultural resources and improving soil health. However, the use of nitrogen (N) in cotton/legume intercropping systems requires further evaluation. In this study, three N fertilization rates (cotton/soybean: 160/20, 320/40 and 480/80 kg N ha−1) incorporating three root barrier systems (complete, semi and no root barrier between the crops) under cotton/soybean intercropping systems were conducted to assess interactions between N supply and N transfer, recovery and residue using the 15N isotope dilution method. The results show that cotton was a stronger competitor for N than soybean plants. The 320/40 kg N ha−1 treatment with no root barrier system inhibited the growth of soybean, while the growth, productivity and N uptake for cotton were maximized. The N fixation rate (%NDFA) in soybean and N transfer rate (%NTFS) from soybean to cotton decreased with the increasing N fertilizer application rate, whereas the intercropping system with no root barrier increased %NDFA and %NTFS. The higher N fertilization rate increased the N residue on the side of cotton, whereas the intercropping with no root barrier increased N utilization rate (%NUR) and reduced N residue rate (%NRR). The N transfer amount (NTA) was positively correlated with cotton yield, dry matter (DM) and N uptake, while NTA was negatively correlated with these indicators for soybean. Overall, cotton/soybean intercropping adapted to the 320/40 kg N ha−1 condition and intercropping with no root barrier system by balancing growth, changing N uptake and regulating N fixation transfer, mitigating the issue of N residue.