The alternate use or blending of fresh and brackish waters can effectively control salt accumulation in the root zone during crop growth. In arid areas with limited freshwater, this method can be enhanced through desalination technologies. The brackish-freshwater sequential irrigation strategy (BFSI) is promoted for its lower salt stress and freshwater amount. However, the dynamics of soil salinity and the optimal proportion of brackish water (P-bw) under the BFSI strategy are unclear. To address this, the HYDRUS (2D/3D) model was calibrated and validated using experimental data from the Hetao Irrigation District in Northern China during 2023-2024. Five irrigation treatments with different P-bw (0 %, 25 %, 50 %, 75 %, 100 %) were evaluated. The model accurately simulated ECe changes (R-2 = 0.96, RMSE = 0.19 dS m(-1)). Higher P-bw was associated with higher ECe and salt stress and lower root length density (RLD). Meanwhile, roots showed salt-avoidance behavior with deeper growth under higher P-bw, especially during the filling stage. The highest ECe and salt stress occurred in the later corn growth stage and the 0-40 cm soil layer. The salt stress index (SSIroot), which accounts for the spatial root distribution, is proposed. The index shows a significant relationship with corn yield than ECe, RLD, and different degrees of salt stress. Scenario analysis revealed that a P-bw of 65 % resulted in the lowest increases in ECe and SSIroot, while RLD and corn yield decreased only by 9.7 % and 14.0 %, respectively. Therefore, a P-bw of 65 % is recommended to maximize brackish water utilization with minimal yield loss.