Enhancing nitrogen (N) use efficiency (NUE) and reducing urea N losses are major challenges in ensuring sustainable agriculture. The aim of this study was to investigate the effect of humic acid urea on N losses, soil microbial nutrient balance and NUE through leaching experiments, soil incubation experiments and field experiments of maize-wheat rotation. We set up four N gradients (240 kg N hm⁻², 216 kg N hm⁻², 192 kg N hm⁻², 168 kg N hm⁻²) and two N fertilizer types (urea and humic acid urea) to make up five treatments, with no N application as the control. The results showed that humic acid urea reduced the fertilizer N losses by 25.51%, 23.07% and 23.08% in the three pathways of N leaching, NH₃ volatilization and N₂O emission, respectively, compared with urea. Humic acid urea significantly increased soil ammonium N, nitrate N and available phosphorus contents, and brought the enzyme stoichiometry ratio closer to 1:1:1, which promoted microbial nutrient balance. Application of humic acid urea significantly increased yield, NUE and annual net economic profit of maize and wheat. Among all treatments, the application of humic acid urea at 216 kg N hm⁻² maximized NUE, reduced environmental pollution and increased yield.