Objective Excessive application of chemical fertilizers threatens soil health, and the combined use of organic and chemical fertilizers is a key pathway to achieving sustainable agricultural development. This study investigates the patterns of soil quality changes under the combined application of organic and chemical fertilizers in the cultivated land of the Yellow River irrigation area in the middle reaches of the Yellow River in Tuoketuo county, Inner Mongolia.

Methods Soil samples were collected from the study area where chemical fertilizers were applied in combination with organic fertilizers for 2−5 years. The chemical properties of the soil and changes in copper and zinc mass fractions were analyzed. Differences in soil chemical properties and copper and zinc mass fractions were compared between different application years of organic fertilizers combined with chemical fertilizers.

Results Compared to soils treated with chemical fertilizers alone, the combined application of chemical fertilizers with organic fertilizers for 2−5 years significantly reduced the pH value of the tillage layer in the study area by 9.33%−16.88% (P < 0.05), decreased electrical conductivity by 35.81%−20.30% (P < 0.05), and significantly reduced water-soluble salts by 62.12%−55.5% (P < 0.05), while soil cation exchange capacity increased significantly by 109.38%−90.61% (P < 0.05). Soil organic matter, total nitrogen, total phosphorus, and available phosphorus increased significantly by 266.36%−491.91%, 140.79%−207.61%, 27.70%−62.94%, and 561.01%−1 123.26% (P < 0.05), respectively. With the improvement of soil fertility, the combined application of organic fertilizer for 2−5 years significantly increased the mass fractions of heavy metals—copper and zinc—in the soil by 376.32%−727.96% and 74.50%−166.86%, respectively (P < 0.05).

Conclusions The combined application of organic and chemical fertilizers reduces soil pH, electrical conductivity, and water-soluble salts, and increases nutrient content, but also enhances copper and zinc accumulation. Therefore, a scientifically sound fertilization plan should be formulated based on regional soil environmental capacity and copper-zinc input flux to achieve the synergistic development of enhanced soil fertility and soil environment protection.