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Aims Humic acid (HA), a soil conditioner, is crucial in saline-alkali soil remediation; however, its effects on saline-alkali soil quality, crop yield, and regulatory mechanisms remain unclear. Methods A 2-year field experiment was conducted, and data from one experimental year were used in this study to explore the effects of different HA application rates (control: 0 Mg ha -1 ; HA3: 3 Mg ha -1 ; HA7.5: 7.5 Mg ha -1 ; HA15: 15 Mg ha -1 ) on soil microorganisms, soil quality, and wheat growth. Results Compared with the control, HA treatment significantly increased soil available potassium (22–45%), available phosphorus (41–53%), and soil organic matter (15–20%), and reduced soil pH (0.1–0.17 units), electrical conductivity (8–27%), chloride ions (3–45%), and sulfate ions (7–34%) in the 0–40 cm soil layer at p < 0.05, which may be associated with the significantly increased abundances of Ascomycota in the rhizosphere soil. HA treatment improved the soil quality index by 22–60% (0–20 cm) and 7–53% (20–40 cm), compared with the control (All p < 0.05). Additionally, the biomass, length, and volume of wheat roots increased by 26–43%, 19–32%, and 18–26%, respectively, which may be attributed to the increase in soil AP content and decrease in pH. These changes may have contributed to the increased in the plant growth index by 15–27%. Regression analysis further confirmed that wheat yield was positively correlated with soil quality and plant growth index. Conclusions These results indicate that HA application may contribute to higher wheat yield by improving soil quality and crop growth, with the most notable effects at HA7.5 and HA15 levels. Based on cost-effectiveness, 7.5 Mg ha -1 (HA7.5) is recommended as the optimal HA application rate for improving saline-alkali soil quality and wheat productivity.