Reservoirs are a category of artificial ecosystem that play a key role in the global carbon cycle. However, there has been limited research on the impacts of dam decommissioning (DD) on greenhouse gas (GHG) emissions over a reservoir life cycle. This study analyzed the effects of DD on CO2 and CH4 fluxes emitted from impounded water zone (area of inundated sediments), the drawdown zone (area of sediment exposure during DD), and the margin zone (area of long-term sediment exposure) before, during, and after the drawdown of a retired reservoir in Inner Mongolia. The margin zone encompassed ± 90 % of the total reservoir area over the study period, whereas the impounded water and drawdown zones accounted for the remainder. CO2 emissions decreased during DD process in the margin zone (325.24 ± 313.80–128.81 ± 128.78 mg m−2h−1) and impounded water zones (286.00 ± 242.00–0.00 ± 0.00 mg m−2h−1), whereas they increased in the drawdown zone (0.00 ± 0.00–239.52 ± 104.35 mg m−2h−1). CH4 emissions gradually declined over time after DD in the impounded water zone and this zone was the main contributor of CH4 fluxes before DD (57.36 ± 12.77 mg m−2h−1), and finally emissions went to zero. Exposure of sediments gradually resulted in a significant increase in CO2 emissions. The major factors affecting GHG emissions were soil volumetric moisture content (SMC) and soil bulk density (ρb). The CO2-eq of the reservoir ecosystem decreased after DD. This happened despite CO2 emissions increasing because CH4, which has a higher global warming potential, decreased following DD. The consideration of DD in the carbon footprint of reservoirs for understanding of reservoir carbon dynamics and the global carbon balance requires further study of the long-term effects of DD on carbon fluxes.