© 2017 Elsevier B.V. The alpine meadows in Qinghai-Tibetan Plateau is an ecosystem sensitive to environmental changes. As part of a study on global climate change and the effects of N precipitation on soil microbiota, we fingerprinted ammonium oxidizing archaea (AOA) and bacteria (AOB) in relation to the N supplement in an alpine meadow in Qinghai-Tibetan Plateau. The results showed that nutrient content in the studied soil was significantly varied in different months (sampling period) but not influenced by the N supplement rate. Long-term nitrogen input dramatically changed the abundance and community composition of the AOB but exerted no obvious effect on the AOA community in the tested soil. Significant differences in the abundance and composition of AOA were recorded in different months. Our findings implied that 1) the soil fertility and physicochemical features of the studied alpine meadows in Qinghai-Tibetan Plateau were stable even under the long-term high N supply; 2) AOB might be the active nitrifiers responding to the high N supply, while the AOA were the abundant and stable nitrifiers despite the N supply; 3) sampling periods mainly affected the abundance and community composition of the nitrifiers in the tested alpine meadow; and 4) the AOB in the studied area are psychrotrophs. Therefore, despite the enhancement of plant growth, high N supplements in the tested alpine meadow ecosystems might cause more pollution to water and air, which in turn contributes to global climate change.