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Freshwater resources are scarce in desert regions. Highly saline groundwater of different salinity is being used to drip irrigate the Taklimakan Desert Highway Shelterbelt with a double- branch-pipe system controlling the irrigation cycles. In this study, to evaluate the dynamics of soil moisture and salinity under the current irrigation system, soil samples were collected to a 2-m depth in the shelterbelt planted for different years and irrigated with different groundwater salinities, and soil moisture and salinity were analyzed. The results showed that both depletion of soil moisture and increase of topsoil salinity occurred simultaneously during one irrigation cycle. Soil moisture decreased from 27.4% to 2.4% for a 15-day irrigation cycle and from 26.4% to 2.7% for a 10-day-cycle, respectively. Topsoil electrical conductivity (EC) increased from 0.64 to 3.32 dS/m and 0.70 to 3.99 dS/m for these two irrigation cycles. With increased shelterbelt age, profiled average soil moisture (0-200 cm) reduced from 12.8% (1-year) to 7.1% (10-year); however, soil moisture in 0-20-cm increased, while topsoil salinity decreased. In addition, irrigation salinity mainly affected soil salinity in the 0-20-cm range. We conclude that water supply with the double-branch-pipe is a feasible irrigation method for the Taklimakan Desert Highway Shelterbelt, and our findings provide a model for shelterbelt construction and sustainable management when using highly saline water for irrigation in analogous habitats.