Soil salinization is a main environmental and ecological problem in irrigated agro-ecosystems especially for the area with shallow groundwater table. Most previous studies mainly focused on the surface and root zone soil salinity, however, the knowledge on spatio-temporal dynamics of soil salinity for both root zone and deep soil as well as driving factors, and the recommended seasonal and annual groundwater depth for salt control was rarely addressed. In this study, 68 cropland sampling experiments and investigations related to soil salinity from the top soil to the depth of 1.80 m, groundwater depth and salinity, and crop types were carried out before and after the crop growing season of 2017-2018 in the Hetao Irrigation District. Soil salinity statistical characteristics showed that the standard deviation of soil salinity in time and space became larger with increasing of temporal mean and spatial mean. The root zone (within depth of 0～0.60 m) soil salinity in the crop growing season were accumulated and desalinated in the fallow season, which was opposite for changes of the deep (within depth of 0.60-1.80 m) soil salinity. The multi-factor variance analysis of variance showed that the driving factors including crop type, groundwater depth at the beginning of crop growing season, averaged groundwater depth in the crop growing season, groundwater salinity and root zone soil salinity at the beginning of crop growing season had significant effects on root zone soil salinity changes in the crop growing season (P<0.05). The influence of groundwater condition and other factors on root zone soil salinity change during crop growing season was closely related to the hydrological year type. At the beginning of crop growing season, the soil salinity in the root zone decreased exponentially with increasing groundwater depth, and the sampling locations with soil salinity below average had a minimum groundwater depth of 1.60 m. Both salt value and salt reduction rate decreased with groundwater depth increased across different soil layers when the average annual groundwater depth was less than 2.50 m. Thus, the sampling locations were selected where the groundwater table depth was less than 2.50 m, and then the median of root zone soil salinity and groundwater depth was obtained by the frequency analysis method. The annual suitable critical control groundwater depth for soil salinity median was 1.77 m. The groundwater depth of sampling locations where soil salinity was significantly higher than the median or mean value were less than 1.77 m. Therefore, in order to control soil salinity, it is recommended that the groundwater depth should be no less than 1.60 m at the beginning of crop growing period, and to maintain an average annual groundwater depth of at least 1.77 m. The research results will provide theoretical support for the design of irrigation scheduling and the rational layout of drainage projects for similar irrigation area in the arid area.