Accurate quantification of evaporation loss from irrigation canals at an irrigation district scale is very useful for developing efficient irrigation strategies, particularly in water-deficient regions. The double-deck surface air layer (DSAL) model, a new aerodynamic method proposed by Kobayashi et al. (2013), is used for estimating the evaporation loss from a running water surface in irrigation canals. In this study, based on the long-term meteorological measurements made at automatic weather stations in 2013 and the field experiment conducted at - midstream areas of the Heihe River Basin (HRB), northwestern China, the DSAL model was applied to estimate the long-term evaporation loss from irrigation canals, which was the remarkable highlight of the study. The results showed that the rate of evaporation from irrigation canals exhibited a concave-up trend for the period from June to September, with higher values in June and September (20 to 50 mm day−1) and lower values in July and August (around 10 mm day−1). During the four months, for the Yingke and Daman irrigation districts in the Zhangye Oasis, the total water losses from irrigation canals due to evaporation were approximately 23.9 × 105 m3 and 36.6 × 105 m3, or 3.2% and 4.8% of the total amount of irrigation water, respectively. Results of the study are not only important for improving the irrigation water use efficiency, but also are beneficial to develop sustainable water resource management in the midstream areas of the HRB.