Freshwater scarcity in arid regions is driving increased use of saline irrigation, yet salinity severely degrades soil structure and suppresses enzymatic function. To address this critical challenge for sustainable soil management, this study systematically evaluated magnetized saline water (MSW) across three salinity levels (1, 3, and 6 g L⁻¹) and four magnetic field strengths (0, 0.2, 0.4, and 0.6 T), confirming the magnetic field intensity (C) × salinity (S) interaction. The comprehensive analysis integrated data on aggregate stability, key ion concentrations (Ca²⁺, Mg²⁺, Cl⁻), and major enzyme activities. Structural Equation Modeling (SEM) was utilized to quantify the underlying mechanisms, demonstrating that structural improvement is primarily driven by strong indirect pathways, mediated by optimized ion dynamics and increased enzyme-mediated organic matter turnover. The moderate-salinity (3 g L⁻¹), moderate-magnetic-field (0.4 T) regime emerged as the optimal balanced strategy for overall soil health. These findings offer a scalable approach, guiding future field-scale research toward long-term agricultural sustainability.