Saline water irrigation is increasingly used in arid regions, but its influence on soil aggregate stability remains uncertain when combined with magnetization pretreatment. A two-year field-pit experiment was conducted during 2024–2025 with four magnetization intensities (0, 0.2, 0.4, and 0.6 T) and three irrigation water salinity levels (≤1, 3, and 6 g L⁻¹). Mechanically stable and water-stable soil aggregates were analyzed in the 0–60 cm soil profile. Magnetization treatments changed aggregate-size distribution, but the dominant response differed between aggregate types. Mechanically stable aggregates mainly showed an increase in the >2 mm fraction and a decrease in the 0.053–0.25 mm fraction, whereas water-stable aggregates mainly showed an increase in the 0.25–1 mm fraction and a decrease in the 0.25 mm (R_0.25), mean weight diameter (MWD), and geometric mean diameter (GMD) varied with soil depth, salinity level, and year. Under S6, C4S6 increased the R_0.25 of mechanically stable aggregates in both years, reaching 73.90% in 2025 compared with 61.60% under C0S6. Correlation and exploratory path analyses suggested that changes in aggregate stability were mainly associated with the redistribution of key aggregate-size fractions. Under the field-pit conditions of this study, some magnetization treatments, particularly 0.4 T, were often associated with higher stability indices than non-magnetized saline irrigation, but this pattern was not consistent across all depths, salinity levels, years, and indicators. Long-term open-field validation is still required.