The study aimed to understand the inter-annual variations of methane (CH(4)) emissions from an open fen on the Qinghai-Tibetan Plateau (QTP) from 2005 to 2007. The weighted mean CH(4) emission rate was 8.37±11.32 mg CH(4) m(-2 )h(-1) during the summers from 2005 to 2007, falling in the range of CH(4) fluxes reported by other studies, with significant inter-annual and spatial variations. The CH(4) emissions of the year of 2006 (2.11±3.48 mg CH(4) m(-2 )h(-1)) were 82% lower than the mean value of the years 2005 and 2007 (13.91±17.80 mg CH(4) m(-2 )h(-1) and 9.44±14.32 mg CH(4) m(-2 )h(-1), respectively), responding to the inter-annual changes of standing water depths during the growing season of the three years. Significant drawdown of standing water depth is believed to cause such significant reduction in CH(4) emissions from wetlands in the year 2006, probably through changing the methanogen composition and decreasing its community size as well as activating methanotrophs to enhance CH(4) oxidation. Our results are helpful to understand the inter-annual variations of CH(4) emission and provide a more reasonable regional budget of CH(4) emission from wetlands on the QTP and even for world-wide natural wetlands under climate change.