Peatlands store large amounts of carbon (C) and actively exchange greenhouse gases (GHGs) with the atmosphere, thus playing an important role in global C cycle and climate. Large uncertainty exists in estimating C and GHG budgets of the alpine peatlands on Qinghai-Tibetan Plateau (QTP), as direct measurements of carbon dioxide (CO2) and methane (CH4) fluxes are still scarce in this region. In this study, we provided ~2.5-year continuous CO2 and CH4 fluxes measured using the eddy covariance technique in a typical alpine peatland on the eastern QTP to estimate the net C and CO2-eq fluxes and investigate their environmental controls. Our results showed that the mean annual CO2 and CH4 fluxes were -106 g C-CO2 m-2 yr-1 and 35 g C-CH4 m-2 yr-1, respectively. While considering the traditional and sustained global warming potentials of CH4 over the 100-year time scale, the peatland acted as a net source of CO2-eq (918 and 1712 g CO2-eq m-2 yr-1, respectively). The net CO2-eq emissions during the non-growing seasons contributed to over 40% of the annual CO2-eq budgets. We further found that the net CO2-eq flux was primarily influenced by soil temperature and global radiation variations. This study was the first assessment to quantify the net CO2-eq flux of the alpine peatland in the QTP region using long-term eddy covariance measurements. Our study highlights that CH4 emissions from peatlands can largely offset the net cooling effect of CO2 uptake and future climate changes such as global warming might further enhance their potential warming effect.