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At high latitudes, winter climate change alters snow cover and, consequently, may cause a sustained change in soil frost dynamics. Altered winter soil conditions could influence the ecosystem exchange of carbon dioxide (CO2) and, in turn, provide feedbacks to ongoing climate change. To investigate the mechanisms that modify the peatland CO2 exchange in response to altered winter soil frost, we conducted a snow exclusion experiment to enhance winter soil frost and to evaluate its short-term (1–3 years) and long-term (11 years) effects on CO2 fluxes during subsequent growing seasons in a boreal peatland. In the first 3 years after initiating the treatment, no significant effects were observed on either gross primary production (GPP) or ecosystem respiration (ER). However, after 11 years, the temperature sensitivity of ER was reduced in the treatment plots relative to the control, resulting in an overall lower ER in the former. Furthermore, early growing season GPP was also lower in the treatment plots than in the controls during periods with photosynthetic photon flux density (PPFD) ≥800 μmol m−2 s−1, corresponding to lower sedge leaf biomass in the treatment plots during the same period. During the peak growing season, a higher GPP was observed in the treatment plots under the low light condition (i.e. PPFD 400 μmol m−2 s−1) compared to the control. As Sphagnum moss maximizes photosynthesis at low light levels, this GPP difference between the plots may have been due to greater moss photosynthesis, as indicated by greater moss biomass production, in the treatment plots relative to the controls. Our study highlights the different responses to enhanced winter soil frost among plant functional types which regulate CO2 fluxes, suggesting that winter climate change could considerably alter the growing season CO2 exchange in boreal peatlands through its effect on vegetation development.The enhanced winter soil frost did not significantly affect the growing season gross primary production (GPP) and ecosystem respiration (ER) in the short term; however, in the long term (i.e. after 11 consecutive winters with enhanced soil frost treatment), the growing season ER was reduced and seasonal pattern of GPP was changed.