Comprehensive seasonal observation is essential for accurately quantifying methane (CH4) emissions from ponds and lakes in permafrost regions. Although CH4 emissions during ice thaw are important and highly variable in high‐latitude freshwater ponds and lakes (north of ∼50°N), their contribution is seldom included in estimates of aquatic‐atmospheric CH4 exchange across different alpine ecosystems. Here, we characterized annual CH4 emissions, including emissions during ice thaw, from ponds and lakes across four alpine vegetation zones in the Qinghai‐Tibet Plateau (QTP) permafrost region. We observed significant spatial variability in annual CH4 emission rates (8.44−421.05 mmol m−2 yr−1), CH4 emission rates during ice thaw (0.26−144.39 mmol m−2 yr−1), and the contribution of CH4 emissions during ice thaw to annual emissions (3−33%) across different vegetation zones. Dissolved oxygen concentration under ice, along with substrate availability and water salinity, played critical roles in influencing CH4 flux during ice thaw. We estimated annual CH4 emissions from ponds and lakes in the QTP permafrost region as 0.04 (0.03−0.05) Tg CH4 yr−1 (median (first quartile−third quartile)), with approximately 20% occurring during ice thaw. Notably, the average areal CH4 emission rate from ponds and lakes in the QTP permafrost region amounts to only 8% of that from high‐latitude waterbodies, primarily due to the dominance of large saline lakes with lower CH4 emission rates in the alpine permafrost region. Our findings emphasize the significance of incorporating comprehensive seasonal observation of CH4 emissions across different vegetation zones in better predicting CH4 emissions from alpine ponds and lakes.