It is necessary to explore the effects of saline water irrigation combined with application of organic fertilizer on water-stable aggregates of plow layer soil. In this study, a long-term saline water irrigation experiment combined with application of organic fertilizer was carried out under winter wheat-summer maize double cropping system. Treatments were set up with four irrigation water salinities (1, 2, 4, 6 g/L) and with organic fertilizer applied (OF) or not (NOF). We measured the effects of different treatments on variation of soil salinity (EC_1:5), soil organic matter (SOM) content and the stability of water-stable aggregates in 0-20 cm soil layer form 2018 to 2019. The results indicated that saline water irrigation tended to increase soil salinity and decrease SOM content and the stability of water-stable aggregates. Meanwhile, with the increasing salinities of irrigation water, SOM content and the mass fraction of water-stable aggregate (>0.25 mm) (WR_0.25), mean weight diameter (MWD) and geometric mean diameter (GMD) decreased; on the contrary, soil EC_1:5 and fractal dimension (D_m) increased. In addition, there were significant differences only between 4 g/L, 6 g/L and 1 g/L treatments. It was found that applying organic fertilizer could reduce EC_1:5 in 0-20 cm soil layer. When the salinity of irrigation water was ≥ 2 g/L, the EC_1:5 of plow layer with organic fertilizer application was 4.64%~48.29% lower than those of treatments without organic fertilizer application. Applying organic fertilizer significantly increased SOM content, WR_0.25, MWD and GMD, with the increases of 80.75%~127.32%, 10.36%~90.44%, 12.90%~129.11% and 11.88%~81.57%. In summary, irrigation water salinity of ≥ 4 g/L could significantly increase soil salinity, reduce organic matter content and destroy soil aggregate structure, so it should be used cautiously. The application of organic fertilizer could promote the salt leaching from the surface soil to the deep layer, reduce the negative impacts of salt on soil environment, and contribute to the safe and efficient utilization of saline water resources.