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.