A future increase in heavy precipitation events is predicted in boreal regions. An irrigation experiment was conducted in Taiga forest in eastern Siberia to evaluate the effect of heavy precipitation on greenhouse gas ([GHG] CO2, CH4, and N2O) fluxes in the soil. The GHG fluxes on the soil surface were measured using a closed-chamber method and GHG production rates in the mineral soil were estimated using the concentration–gradient method based on Fick’s law. Irrigation water (20 mm day−1) was applied continuously for 6 days (120 mm in total; the same amount as summer precipitation in this region). Greenhouse gas production rates in the organic layer (O-layer) were defined as the difference between the GHG fluxes and the GHG production rates in the mineral soil. Carbon dioxide flux was measured both in root-intact (Rs) and trenched plots (Rmw). The root respiration rate (Rr) was calculated as the difference between Rs and Rmw. Considering the root distribution in the soil, we regarded the CO2 production rate in the mineral soil to be the microbial respiration rate in the mineral soil (Rmm) and microbial respiration rate in the O-layer (Rmo) as the difference between Rmw and Rmm. Irrigation increased both soil temperature and moisture in the irrigated plot. The Rs, CH4 flux and N2O flux during the irrigation period were higher in the irrigated plot than that in the non-irrigated plot (P < 0.05; mean Rs ± standard deviation [SD] (mg C m−2 h−1) were 171 ± 20 and 109 ± 11, mean CH4 flux ± SD (μg C m−2 h−1) were −5.4 ± 4.1 and −14.0 ± 6.5, and mean N2O flux ± SD (μg N m−2 h−1) were 1.6 ± 1.6 and 0.2 ± 1.1, respectively). Soil moisture had a positive effect on Rmm and CH4 production rate in the O-layer, a negative effect on Rr, and did not affect Rmo, the CH4 production rate in the mineral soil or the N2O production rates in both the O-layer and the mineral soil. Soil temperature had a positive effect on Rr and Rmo. The increment of global warming potential of the soil mainly resulted from an increase in microbial respiration rates. Future changes in precipitation patterns in this region would accelerate decomposition of the soil organic matter.