Soda saline–alkaline soils have seriously restricted the sustainable development of agriculture in the Songnen Plain, China. Applying soil amendments has proven to be an effective remediation strategy for these sodic soils; however, conventional amendments face limitations, including prolonged remediation periods and the potential to cause secondary pollution upon misapplication. In this study, we combined three different amendments and applied them as four distinct treatments—citric acid + nano-silica (CS), citric acid + nano-silica + humic acid (CSH), nano-silica + humic acid (SH), and citric acid + humic acid (CH)—with no amendment used as the control (CK). The effects of these treatments on improving the soda saline–alkali soil was evaluated using a field positioning experiment. The results indicate that, compared to the CK treatment, applying the amendments significantly increased the concentrations of available phosphorus (AP) (9.19% to 44.43%) and organic matter (SOM) (3.53% to 16.48%) while decreasing alkalinity and salinity indicators (pH, EC (electrical conductivity), ESP (exchangeable sodium percentage), SAR (sodium adsorption ratio), and TA (total alkalinity)) and soil alkali stress ions (water-soluble and exchangeable Na⁺, CO₃²⁻, and HCO₃⁻). The partial least squares path modeling analysis (PLS-PM) demonstrated that the application of the amendments improved soil quality by changing its alkalinity and ion composition, thereby increasing the maize yield (from 3.01% to 9.80%).