Soil salinization and desalinization are complex processes caused by natural conditions and human-induced risk factors. Conventional salinity risk identification and management methods have limitations in spatial data analysis and often provide an inadequate description of the problem. The objectives of this study were to identify controllable risk factors, to provide response measures, and to design management strategies for salt-affected soils. We proposed to integrate spatial autoregressive (SAR) model, multi-attribute decision making (MADM), and analytic hierarchy process (AHP) for these purposes. Our proposed method was demonstrated through a case study of managing soil salinization in a semi-arid region in China. The results clearly indicated that the SAR model is superior to the OLS model in terms of risk factor identification. These factors include groundwater salinity, paddy area, corn area, aquaculture (i.e., ponds and lakes) area, distance to drainage ditches and irrigation channels, organic fertilizer input, and cropping index, among which the factors related to human land use activities are dominant risk factors that drive the soil salinization processes. We also showed that ecological irrigation and sustainable land use are acceptable strategies for soil salinity management.