An incubation experiment was conducted to examine the effects of nitrogen (N) application on microbial respiration in alpine meadow and alpine shrub soils from eastern of Qinghai-Tibetan Plateau. Four different levels of nitrogen fertilization were selected in this study: control (CK, 0 mg N g(-1)), low (LN, 0.04 mg N g(-1)), medium (MN, 0.16 mg N g(-1)), high (HN, 0.4 mg N g(-1)). The results showed that microbial respiration was higher in alpine shrub than in alpine meadow soil, regardless of the rate of N application. Total microbial respiration over the course of incubation period decreased in both soils with HN and MN treatments relative to control, but no significant differences were observed in soils with LN treatments. There was significantly positive correlation between total microbial respiration and dissolved organic carbon concentration in both soils. The results indicated that DOC may be a useful indicator of microbial respiration rate in alpine soils and the increasing N inputs could drive a negative feedback to global warming effects of carbon dioxide emitted to the atmosphere in alpine soils.