This study used mesocosms to examine the effects of alternate drying and rewetting on CO2 and CH4 emissions from high-altitude peatlands on the Tibetan Plateau. The drying and rewetting experiment conducted in this study included three phases: a 10-day predrying phase, a 32-day drying phase, and an 18-day rewetting phase. During the experiment, the water table varied between 0 and 50 cm with respect to the reference peat column where the water table stayed constant at 0 cm. The study found that drying and rewetting had no significant effect on CO2 emissions from the peatland, while CH4 emissions decreased. The cumulative CH4 emissions in the control group was 2.1 times higher than in the drying and rewetting treatment over the study period. Moreover, CO2 and CH4 emissions were positively correlated with soil temperature, and the drying process increased the goodness of fit of the regression models predicting the relationships between CO2 and CH4 emissions and temperature. These results indicate that small-scale water table variation has a limited effect on CO2 emissions, but might reduce CH4 emissions in high-altitude peatlands on the Tibetan Plateau.