In this study, a long-term saline water irrigation experiment was carried out on wheat-maize farmland since 2006, and studied the change characteristics of soil salinity (EC_e), water-stable aggregates particle size distribution and their stability index under the condition of continuous saline water irrigation with different salinity in the 13th and14th year (in 2018 and 2019). Five salinity levels of irrigation water were tested:2 (T1), 4 (T2), 6 (T3), and 8 (T4), and fresh groundwater (1 g/L) was used as control treatment (CK). The salinity level from T1 to T4 was formed by mixing sea salt into the freshwater. The results showed that saline water irrigation increased soil EC_e. Compared with CK, the EC_e in the treatment of 2 g/L showed no significant difference, but a significant increase when the salinity of irrigation water beyond 4 g/L. Saline water irrigation affected the particle size distribution of soil water-stable aggregates. When the salinity of irrigation water was less than 4 g/L, the macroaggregate (>0.25 mm) was the dominant particle size of soil water stable aggregates in 0—40 cm soil layer. With the increase of irrigation water salinity, the mass fraction of macroaggregate decreased, while the mass fraction of microaggregate (0.053~0.25 mm) and silt + clay aggregate (<0.053 mm) increased. When the salinity of irrigation water reached 6 g/L, silt + clay aggregate was dominant in 0—40 cm soil layer. With the increase of irrigation water salinity, the average weight diameter (MWD) and geometric mean diameter (GMD) of soil aggregates decreased, while the fractal dimension (D) increased, which meant that the stability of soil water stable aggregates decreased. Under this irrigation system, saline water with salinity greater than or equal to 4 g/L significantly increased soil salinity and destroyed soil aggregate structure, which should be used cautiously in the irrigation of wheat-maize crop system.