To understand the seasonality of methane flux from alpine wetlands in Zoige Plateau, 30 plots were set to measure the methane emissions in the growing and nongrowing seasons in three environmental types: dry hummock (DH), Carex muliensis (CM), and Eleocharis valleculosa (EV) sites. There were clearly seasonal patterns of methane flux in different environmental types in the growing and nongrowing seasons. Mean methane emission rate was 14.45 mg CH4 m−2 h−1 (0.17 to 86.78 mg CH4 m−2 h−1) in the growing season, and 0.556 mg CH4 m−2 h−1 (0.002 to 6.722 mg CH4 m−2 h−1) in the nongrowing season. In the growing season, the main maximum values of methane flux were found in July and August, except for a peak value in September in CM sites. In the nongrowing season, the similar seasonal variation pattern was shared among all the three sites, in which the methane emissions increased from February to April. In the growing season, the determining factors were surface temperatures (r2 = 0.55, P < 0.05), standing water depths (r2 = 0.32, P < 0.01) and plant community heights (r2 = 0.61, P < 0.01), while in the nongrowing season, ice thickness (r2 = 0.27, P < 0.05; in CM and EV sites) was found most related to flux. In our understanding, the seasonality of methane emissions in our study areas was temperature- and-plant-growth-dependent, and the water table position was also very important to shape the temperature-and-plant-growth-dependent seasonal variation of flux with its vigorous variations in alpine wetland ecosystems. Different environmental types within the wetland also influenced the seasonal pattern of methane flux. For an accurate estimate of the global methane source strength of alpine wetlands, the pronounced seasonal or even temporal variability in methane emission from alpine wetlands should be taken into consideration.