Permafrost thaw and its impacts on ecosystem carbon (C) dynamics are critical for predicting global climate change. It remains unclear whether annual and seasonal warming (winter or summer) affect permafrost thaw and ecosystem C balance differently. It is also required to compare the short-term stepwise warming and long-term gradual warming effects. This study validated a land surface model, the Community Atmosphere Biosphere Land Exchange model, at an Alaskan tundra site, and then used it to simulate permafrost thaw and ecosystem C flux under annual warming, winter warming, and summer warming. The simulations were conducted under stepwise air warming (2°C yr−1) during 2007–2011, and gradual air warming (0.04°C yr−1) during 2007–2056. We hypothesized that all warming treatments induced greater permafrost thaw, and larger ecosystem respiration than plant growth thus shifting the ecosystem C sink to C source. Results only partially supported our hypothesis. Climate warming further enhanced C sink under stepwise (6–15%) and gradual (1–8%) warming scenarios as followed by annual warming, winter warming, and summer warming. This is attributed to disproportionally low temperature increase in soil (0.1°C) in comparison to air warming (2°C). In a separate simulation, a greater soil warming (1.5°C under winter warming) led to a net ecosystem C source (i.e., 18 g C m−2 yr−1). This suggests that warming tundra can potentially provide positive feedbacks to global climate change. As a key variable, soil temperature and its dynamics, especially during wintertime, need to be carefully studied under global warming using both modeling and experimental approaches.