Soil salinization and water scarcity severely constrain sustainable agricultural production worldwide. Freezing saline water irrigation (FSWI) is a promising approach for utilizing unconventional water resources to rehabilitate saline-alkali soils, yet its ecological mechanisms remain insufficiently understood. Here, we conducted a field experiment in a typical arid region using four irrigation intensities (0, 90, 180, and 270 mm) and examined microbial and functional dynamics across the freeze-thaw cycle using high-throughput sequencing, cooccurrence network analysis, a soil multifunctionality index, and structural equation modeling (SEM). The results show that FSWI reshaped key abiotic conditions by regulating salt redistribution and transport, improving soil structure, and enhancing nutrient cycling, which correspond to the SEM modules of Salt Transport, Structure Change, and Nutrient Cycling, respectively; these abiotic shifts drove deterministic microbial succession and reorganization of microbial interaction networks. Among the tested intensities, FSWI180 was optimal under the conditions of this study, producing the highest microbial diversity, network complexity, and network stability. SEM further indicated that strengthened nutrient cycling and improved soil structure under FSWI180 promoted microbial diversity and network complexity, which helped offset negative effects associated with salt transport and ultimately increased soil multifunctionality. Overall, this study proposes a microbial-mediated mechanism in which moderate FSWI-induced environmental regulation promotes microbial community reconfiguration and thereby supports coordinated improvements in soil functions, providing an ecological basis for optimizing FSWI management in saline-alkali croplands in arid regions.