Abstract: Soil salinization and secondary salinization have often occurred in the Yellow River irrigation area of northern Ningxia, China. As such, the regional food security is seriously constrained in sustainable agriculture. However, existing research has focused mainly on a single improvement. In this study, a systematic comparison was made of the different organic amendments on the water-salt transport, nutrient dynamics, and crop physiological responses. Three organic amendments were selected from the humic acid (HA), carboxymethyl cellulose (CMC), and amino acids (AA). Their efficacy was also evaluated to regulate the soil physicochemical properties and maize productivity. Specific regulatory mechanisms of these amendments were determined in deep soil. The optimal technical patterns were identified for the ecological restoration and yield enhancement of the saline-alkali land in the arid irrigation areas. A continuous three-year experiment of the field positioning was conducted from April 2022 to September 2024. A typical saline-alkali region was taken from the Pingluo County, Shizuishan City, Ningxia Hui Autonomous Region, China. 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 were measured, including the soil gravimetric water content, saturated paste extract electrical conductivity (ECe), pH, sodium adsorption ratio (SARe), alkali-hydrolyzable nitrogen, available phosphorus, available potassium, and soil organic carbon. Additionally, some indicators were monitored annually, including the maize photosynthesis, agronomic traits, aboveground biomass, grain yield, and water use efficiency (WUE). Economic benefits were calculated using input costs and crop output values. The results indicated that all organic amendments were significantly optimized after the soil microenvironment, compared with the control. 1) The CMC treatment exhibited the strongest water retention capacity in the plow layer (0-40 cm) after the formation of a hydrophilic gel network. Among them, surface evaporation and deep percolation were significantly reduced by 40.49%. This physical barrier also inhibited the salt leaching in deeper layers. In contrast, the HA treatment demonstrated the most effective desalination. Cation exchange was also enhanced to displace the sodium ions. The HA was achieved in a desalination rate of 26.2%-35.1% in the 0-50 cm active root zone, compared with the CK. While the soil SARe was reduced by 18.9%. 2) All amendments significantly enhanced the soil fertility, where the soil organic carbon, alkali-hydrolyzable nitrogen, and available potassium contents also increased by 13.9%-57.0% over the 0-100 cm profile. The HA and AA treatments improved the nutrient availability, whereas the nutrient activation of the CMC was relatively lower. 3) While the amendments failed to significantly alter the vegetative traits, such as the plant height or stem diameter, they markedly improved the reproductive output.The average grain yield reached 13499 kg/hm² after 3 years of humic acid treatment, which was 27.67% higher than the control treatment, and the water use efficiency reached 24.46 kg/(hm²·mm). 4) The HA treatment also yielded the highest net income (21677.60 Yuan/hm²) and input-output ratio (3.04). Although the AA treatment increased the yield, the high marginal cost significantly lowered the input-output ratio (2.12), thus limiting its economic viability as a standalone amendment. In conclusion, the regulatory mechanisms were identified for the three amendments under saline-alkali conditions. Humic acid was the optimal choice for soil improvement. The sodium was effectively displaced to improve the soil structure and economic returns. Moreover, carboxymethyl cellulose was also required to prevent the deep-layer salt accumulation, suitable for the water-scarce areas. Amino acids served as the nutrient activators, indicating the economic constraints for the large-scale application. Future strategies should focus on the synergistic optimization of humic acid with the low-cost amendments in the Yellow River irrigation area, particularly for the cost-effectiveness and ecological benefits.