With climate change, Nitrogen deposition (ND) and carbon dioxide (CO2) have increased significantly, but the effects of ND and CO2 fertilization on carbon-use efficiency (CUE) and water-use efficiency (WUE) are still unclear. Therefore, the effects of ND and CO2 on CUE and WUE are studied by means of trend analysis and partial derivatives. The results show the following: (1) From 2000 to 2020, the mean CUE in China was 0.533, and the WUE was 1.235 g C kg−1 H2O. (2) In the study area, a 53.8% CUE and 61.8% WUE showed an upward trend, and ND enhanced the positive contribution of CO2 to CUE and WUE by 15.9% and 19.3%, respectively. (3) ND explained 48.1% and 56% of the increase in CUE and WUE, respectively, and CO2 explained 45.8% and 50.1% of the increases in CUE and WUE, respectively. (4) The areas dominated by ND and CO2 accounted for 43.9% and 12.7% of the total area, respectively, highlighting the importance of ND in the driving mechanism of CUE and WUE. The research results are helpful to further research in CUE and WUE.