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Arid and semi-arid ecosystems represent a crucial but poorly understood component of the global water cycle. Taking a desert ecosystem as a case study, we measured sap flow in three dominant shrub species and concurrent environmental variables over two mean growing seasons. Commercially available gauges (Flow32 meters) based on the constant power stem heat balance (SHB) method were used. Stem-level sap flow rates were scaled up to stand level to estimate stand transpiration using the species-specific frequency distribution of stem diameter. We found that variations in stand transpiration were closely related to changes in solar radiation (Rs), air temperature (T), and vapor pressure deficit (VPD) at the hourly scale. Three factors together explained 84% and 77% variations in hourly stand transpiration in 2014 and 2015, respectively, with Rs being the primary driving force. We observed a threshold control of VPD (~2 kPa) on stand transpiration in two-year study periods, suggesting a strong stomatal regulation of transpiration under high evaporative demand conditions. Clockwise hysteresis loops between diurnal transpiration and T and VPD were observed and exhibited seasonal variations. Both the time lags and refill and release of stem water storage from nocturnal sap flow were possible causes for the hysteresis. These findings improve the understanding of environmental control on water flux of the arid and semi-arid ecosystems and have important implications for diurnal hydrology modelling.