Nitrogen (N) deposition has become an important factor of vital changes in the Qinghai-Tibetan Plateau (QTP), one of the key eco-regions in the world. To investigate how N deposition affects the fluxes of GHGs (CH4, CO2, N2O) in the alpine grassland ecosystem, the dominant ecosystems on QTP, we conducted control experiments in three types of alpine grasslands, including the alpine meadow (AM), alpine steppe (AS), and cultivated grassland (CG) on the QTP. In this study, four N addition gradients (0 kg Nha−1yr−1, 8 kg Nha−1yr−1, 24 kg Nha−1yr−1, and 40 kg Nha−1yr−1) were set up using ammonium nitrate from 2015 to 2020 in order to simulate N deposition at different levels, and after 6 years of continuous N application, greenhouse gases were collected from sampling plots. The results showed that simulated N deposition had no significant effect on soil GHG fluxes, while the grassland type had an extremely significant effect on soil GHG fluxes. Under the same N deposition conditions, the CH4 absorption in the cultivated grassland was higher than that in the other two types of grasslands. At low N deposition levels (CK, N1), the CO2 emission in the cultivated grassland was higher than that in the other two types of grasslands. At high N deposition levels (N2 and N3), the N2O emission in the cultivated grassland increased more significantly than it did in the other two types of grasslands. Control of grassland cultivation should be proposed as a reliable form of land-use management to reduce GHG emissions on the QTP in the era of increasing N deposition.