Soil salinization and water deficits are considered the primary factors limiting economic development and environmental improvement in arid areas. However, there remains limited knowledge of the adaptability of typical shrubs to salinization of desert areas in arid zones. This study was conducted in a desert oasis transition zone (Tarim River, China), aiming to investigate: i) the spatial-temporal changes in soil salinity; ii) the interactions between the pedoenvironment vs typical shrub (Calligonum mongolicum). The van Genuchten soil salinity retention ensemble model (TVGSSREM-3D) was developed to simulate variations in soil water-salt transport in the desert-oasis zone and to accurately explain the main factors influencing Calligonum mongolicum desert-oases transition areas. The results showed that monthly average salinity ranged from 2.0 to 8.0 g kg−1, with a peak in August (9.17 g kg−1). The presence of human activities (Salt Drainage Canal) and the distribution of Calligonum mongolicum resulted in a clear spatial salinity zonation. Moreover, analysis of environmental indicators using the TVGSSREM-3D model revealed strong correlations between the distribution of salinity in Calligonum mongolicum desert-oases transition areas and groundwater depth (GD), minimum relative humidity (MRH), and water vapor pressure (WVP). These findings provide a scientific basis for stabilizing, restoring, and reconstructing the ecosystem of the oasis-desert transition zone.