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Accurate measurement and estimation of crop evapotranspiration (ET) plays an important role in understanding field soil water cycle and managing water-saving irrigation in the arid regions. This study compares three methods for estimating ET: field Water Balance (WB), Eddy Covariance (EC) and Bowen Ratio-Energy Balance (BREB). The experiment was conducted in a vineyard in the arid desert regions of northwest China. Results indicate that the three methods provided similar estimate of total ET. Compared to total ET measured by WB (ETWB) during the whole growing stage, total ET estimated by EC (ETEC) was 1.57% lower, and total ET estimated by BREB (ETBREB) was 5.19% higher. Variations of ETEC and ETBREB are similar at hourly or daily timescale, but the values are slightly different. At sunrise or sunset, ETBREB increases or decreases more rapidly than ETEC. The difference between ETBREB and ETEC is linearly related to the residual of the energy balance for EC and the two methods yielded close estimates when the residual was small. This study showed that the three methods provided accurate estimates of ET at daily and seasonal timescales and the methods can be used to estimate ET from vineyards in arid environments.