To understand spatial and temporal variations of nitrous oxide (N2O) fluxes, we chose to measure N2O emissions from three plant stands (Kobresia tibetica, Carex muliensis, and Eleocharis valleculosa stands) in an open fen on the northeastern Qinghai–Tibetan plateau during the growing seasons from 2005 to 2007. The overall mean N2O emission rate was about 0.018 ± 0.056 mg N m−2 h−1 during the growing seasons from 2005 to 2007, with highly spatiotemporal variations. The hummock (K. tibetica stand) emitted N2O at the highest rate about 0.025 ± 0.051 mg N m−2 h−1, followed by the hollow stands: the E. valleculosa stand about 0.012 ± 0.046 mg N m−2 h−1 and the C. muliensis stand about 0.017 ± 0.068 mg N m−2 h−1. Within each stand, we also noted significant variations of N2O emission. We also observed the significant seasonal and inter-annual variation of N2O fluxes during the study period. The highest N2O emission rate was all recorded in July or August in each year from 2005 to 2007. Compared with the mean value of 2005, we found the drought of 2006 significantly increased N2O emissions by 104 times in the E. valleculosa stand, 45 times in K. tibetica stand, and 18 times in the C. muliensis stand. Though there was no significant relation between standing water depths and N2O emissions, we still considered it related to the spatiotemporal dynamics of soil water regime under climate change.