In order to realize the coordinated development of vegetation in farmland and desert areas, the law of soil water and salt transport in the aeration zone of farmland desert transition zone was studied by in-situ experiment at a test site in the lower reaches of Shiyang River Basin.The results showed that water and salt transport in soil aeration zone in desert area was affected by farmland irrigation. After irrigation, soil salt in farmland area entered groundwater with irrigation water, and then flowed to desert area. It caused the salt content of surface soil in desert area to increase greatly. After water level regulation, irrigation in farmland had a better effect on surface soil desalination, and salt moved deeper downward with irrigation water. After the regulation of the desert area, not only the salt flowing into the desert area from the farmland area was reduced,. but also the salt in the groundwater entering the aeration zone soil was reduced, which effectively alleviated the salt accumulation effect of the surface soil in the desert area.