The Qinghai–Tibet Plateau is a sensitive area of global climate changes, and riparian ecosystems are thought as “hotspots” for climate change adaptation, but little work has been conducted regarding the alpine riparian ecosystems on the Qinghai–Tibet Plateau. We measured evapotranspiration (ET) and surface energy fluxes over the riparian shrub Myricaria squamosa Desv., which is widely distributed on the Qinghai–Tibet Plateau but has not been studied until now. The results indicated that annual ET was 390 mm and 503 mm for the period of 2010 to 2011 and 2011 to 2012, respectively, which was higher than the amount of precipitation during the same period. Cumulative ET was lower than the cumulative reference evapotranspiration during the entire experimental period, whereas ET in August was higher than reference evapotranspiration. ET in the growing season occupied over 80% of annual ET with a maximum daily ET of 7.2 mm d−1, and the ET in the non-growing season was quite low because of the frozen soil. In general, temperature and net radiation were the key variables controlling daily ET rates for M. squamosa. Annual sensible heat flux (H) consumed 60% of net radiation (Rn) and latent heat flux (LE) 40% during the three years of the study. LE occupied the main part of Rn from July to September. H was the highest in May and June, then sunk in the mid-growing season, and rebounded the other peak at late September and early October. Daily ground heat flux was positive from April to midSeptember, and it was an important heat source of land surface in the winter and spring. This study highlighted that as an alpine riparian ecosystem in a semiarid region, ET and surface energy partitioning of the M. squamosa community are strongly affected by the freeze–thaw cycle, groundwater fluctuation, precipitation pulses and soil water content. We speculate that climate warming has a significant impact on ET process and surface energy partitioning of the M. squamosa community by influencing the freeze–thaw cycle and soil water content.