Abstract: Soil salinization and secondary salinization in the Yellow River irrigation area of northern Ningxia significantly constrain regional agricultural sustainability and food security. Existing research has often focused on single improvement measures, lacking a systematic comparison of different organic amendment types regarding their specific regulatory mechanisms on deep soil water-salt transport, nutrient dynamics, and crop physiological responses. This study aimed to evaluate the efficacy of three distinct organic amendments—humic acid (HA), carboxymethyl cellulose (CMC), and amino acids (AA)—in regulating soil physicochemical properties and maize productivity. The ultimate goal was to elucidate the differential mechanisms of these amendments and identify optimal technical patterns for the ecological restoration and yield enhancement of saline-alkali land in arid irrigation districts. A continuous three-year field positioning experiment was conducted from April 2022 to September 2024 in a typical saline-alkali region of Pingluo County, Ningxia. A randomized complete block design was employed with four treatments: unamended control (CK), humic acid (HA, 1500 kg/hm²), carboxymethyl cellulose (CMC, 200 kg/hm²), and amino acids (AA, 1500 kg/hm²). Soil samples were collected from the 0–100 cm profile in 10 cm increments during the maize jointing, tasseling, and milking stages. Key parameters measured included soil gravimetric water content, saturated paste extract electrical conductivity (EC_e), pH, sodium adsorption ratio (SAR_e), alkali-hydrolyzable nitrogen, available phosphorus, available potassium, and soil organic carbon. Additionally, maize photosynthetic characteristics, agronomic traits, aboveground biomass, grain yield, and water use efficiency (WUE) were monitored annually. Economic benefits were calculated based on input costs and crop output values. The three-year data indicated that all organic amendments significantly optimized the soil microenvironment compared to the control. 1) CMC treatment exhibited the strongest water retention capacity in the plow layer (0～40 cm), significantly reducing surface evaporation by 40.49% and deep percolation by approximately 43% through the formation of a hydrophilic gel network. However, this physical barrier inhibited salt leaching in deeper layers. In contrast, HA treatment demonstrated the most effective desalination capability. By enhancing cation exchange and displacing sodium ions, HA achieved a desalination rate of 26.2%～35.1% in the 0～50 cm active root zone and reduced the soil SARe by 18.9% relative to CK. 2) All amendments significantly enhanced soil fertility, with soil organic carbon, alkali-hydrolyzable nitrogen, and available potassium contents across the 0～100 cm profile increasing by 13.9%～57.0%. HA and AA treatments were superior in improving nutrient availability, whereas the nutrient activation effect of CMC was relatively lower. 3) While amendments did not significantly alter vegetative traits like plant height or stem diameter, they markedly improved reproductive output. HA treatment resulted in the highest three-year average grain yield of 13,499 kg/hm², representing a 27.67% increase over CK, and achieved the highest water use efficiency of 24.46 kg/(hm²·mm). 4) HA treatment yielded the highest net income (21,677.60 Yuan/hm²) and input-output ratio (3.04). Conversely, while AA increased yield, its high marginal cost resulted in a significantly lower input-output ratio (2.12), limiting its economic viability as a standalone amendment. In conclusion, distinct regulatory mechanisms were identified for the three amendments under saline-alkali conditions. Humic acid effectively displacing sodium, improving soil structure, and maximizing economic returns, making it the optimal choice for soil improvement in this region. Carboxymethyl cellulose suitable for water-scarce areas, but requires careful management to prevent deep-layer salt accumulation. Amino acids served as nutrient activators but are economically constrained for large-scale independent application. Future strategies should focus on the synergistic compounding of humic acid with low-cost amendments to further optimize cost-effectiveness and ecological benefits in the Yellow River irrigation area.