Very few comparative studies of nitrogen (N) deposition in agroecosystems have been conducted along landuse and altitude gradients. In an effort to fill this gap of knowledge we selected three typical, interconnected landuse systems (cropland, mountain grassland and plain grassland)at six sampling sites in the transboundary Altay Mountains of NW China and SW Mongolia to compare the dynamics and amounts of wet and dry N deposition. During 12 months from June 2014 to May 2015 dry and wet N deposition through middle volume total suspended particulates (TSP), passive samplers and precipitation collectors were monitored. The croplands had the highest concentrations of NH<sub>4</sub><sup>+</sup>-N (1.6 mg N L<sup>−1</sup> in China and 2.0 mg N L<sup>−1</sup> in Mongolia) and of NO<sub>3</sub><sup>−</sup>-N (1.0 mg N L<sup>−1</sup> in China and 1.2 mg N L<sup>−1</sup> in Mongolia) in precipitation compared with the other land use types for wet deposition. In contrast, the Mongolian mountain grasslands experienced the highest wet deposition (3.2 kg N ha<sup>−1</sup> yr<sup>−1</sup>) which was at least partly due to higher summer precipitation (161 mm), the second highest wet deposition occurred on Chinese cropland with 3.1 kg N ha<sup>−1</sup> yr<sup>−1</sup> while wet deposition in other landuse types ranged from 1.8 to 2.5 kg N ha<sup>−1</sup> yr<sup>−1</sup>. Chinese cropland had the highest NH<sub>3</sub> (3.1 μg N m<sup>−3</sup>) and NO<sub>2</sub> (3.8 μg N m<sup>−3</sup>) concentrations and dry N deposition (15.3 kg N ha<sup>−1</sup> yr<sup>−1</sup>) among all landuse types while Mongolian cropland had dry N deposition of 8.9 kg N ha<sup>−1</sup> yr<sup>−1</sup>. Chinese cropland (18.4 kg N ha<sup>−1</sup> yr<sup>−1</sup>) had the highest total N deposition, followed by the Mongolian cropland with 10.7 kg N ha<sup>−1</sup> yr<sup>−1</sup> and the Mongolian mountain grassland with 10.5 kg N ha<sup>−1</sup> yr<sup>−1</sup>. NH<sub>4</sub><sup>+</sup>-N concentration were negatively correlated with precipitation (<i>P</i> < 0.05). Concentration of NH<sub>3</sub> correlated positively with air temperature (<i>P</i> < 0.05) likely reflecting promoting effects of temperature on NH<sub>3</sub> emissions whereas NO<sub>2</sub> correlated negatively with temperature. Over all, croplands in China had 72 % higher N deposition than in Mongolia whereas the reverse was true for mountain grasslands which received 31 % more Nin Mongolia.