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In the face of global climate change, changes in nitrogen use efficiency (NUE) have not been widely considered to affect agricultural productivity. A modeling study was conducted to assess the impacts of future climates on crop yields and NUE in two wheat (Triticum aestivum L.) and maize (Zea mays L.) rotation systems and one continuous maize system in northern China. Specifically, the process-based SPACSYS model was used to predict crop yields and NUE by 2100, under four climate scenarios (Baseline, RCP2.6, RCP4.5 and RCP8.5). The model was validated using data from three long-term experiments, each of which included four fertilization practices typical of the regions: non-fertilizer, combined mineral N, phosphorus (P) and potassium (K) (NPK), NPK plus manure and NPK plus straw. Validation showed SPACSYS well-simulated crop yields and N uptake (R-2: 0.41-0.96; RMSE: 6-18%; and EF: 0.41-0.93). Under future climate change, the model predicted changes in maize yield by - 30.69% and 5.98% in northwestern and northeastern China, respectively, and wheat yield by - 16.37% in northwestern China. Future climates would cause greater NUE reductions in the northwest (wheat: 42.79%; maize: 33.73%) than in the northeast (maize: 3.97%) with smaller decreases in crop N uptake and N loss. Furthermore, manure application had higher crop NUEs (wheat: 6.66-31.27%; maize: 23.82-68.19%) and N uptakes than other treatments under future climate change. The results demonstrated the risks of future climate changes on crop yield and NUE in the study regions and can also help target fertilization practices for effectively mitigating climate change.