Responses of ecosystem carbon (C) fluxes to human disturbance and climatic warming will affect terrestrial ecosystem C storage and feedback to climate change. We conducted a manipulative experiment to investigate the effects of warming and clipping on soil respiration (Rs), ecosystem respiration (ER), net ecosystem exchange (NEE) and gross ecosystem production (GEP) in an alpine meadow in a permafrost region during two hydrologically contrasting years (2012, with 29.9% higher precipitation than the long-term mean, and 2013, with 18.9% lower precipitation than the long-tem mean). Our results showed that GEP was higher than ER, leading to a net C sink (measured by NEE) over the two growing seasons. Warming significantly stimulated ecosystem C fluxes in 2012 but did not significantly affect these fluxes in 2013. On average, the warming-induced increase in GEP (1.49 µ mol m(-2) s(-1)) was higher than in ER (0.80 µ mol m(-2) s(-1)), resulting in an increase in NEE (0.70 µ mol m(-2) s(-1)). Clipping and its interaction with warming had no significant effects on C fluxes, whereas clipping significantly reduced aboveground biomass (AGB) by 51.5 g m(-2) in 2013. These results suggest the response of C fluxes to warming and clipping depends on hydrological variations. In the wet year, the warming treatment caused a reduction in water, but increases in soil temperature and AGB contributed to the positive response of ecosystem C fluxes to warming. In the dry year, the reduction in soil moisture, caused by warming, and the reduction in AGB, caused by clipping, were compensated by higher soil temperatures in warmed plots. Our findings highlight the importance of changes in soil moisture in mediating the responses of ecosystem C fluxes to climate warming in an alpine meadow ecosystem.