Soil salinization significantly threatens sustainable agriculture in arid and semi-arid regions, where improper subsurface drainage layouts often fail to remove harmful ions that inhibit crop growth. Field investigation and laboratory experiments reveal that subsurface pipe drainage (SPD) reduces the content of major ions and enhances crop coverage significantly, with low coverage areas decreasing by 27.4 % and high coverage areas increasing by 13.5 % after SPD installation. Ion-specific leaching efficiencies were found to vary, with sodium (Na+) and chloride (Cl-) removal exceeding 65 %, while magnesium (Mg2+) and bicarbonate (HCO3-) played key roles in improving crop coverage. However, excessive leaching of Mg2+ in high coverage areas reduced its positive effects. The HYDRUS-2D model, calibrated and validated with experimental data, achieved high accuracy in simulating cumulative drainage and ion discharge (R-2 > 0.7 for all ions), with an average root mean square error (RMSE) for major ions below 0.2 g kg(-1). Scenario analysis evaluated 96 configurations of SPD depth, spacing, and leaching quotas. Results indicate that burial depths of 1.4-1.8 m, drainage spacings of 20-30 m, and leaching quotas of 400-500 mm are optimal for balancing salt removal and crop coverage improvement. Configurations targeting major ions, such as Mg2+ and HCO3-, outperformed traditional designs based on total salt reduction, with coverage improvement exceeding 16 % in low-coverage areas. These findings provide actionable strategies for precision salt management and sustainable agriculture in salinized regions.