Abstract: Background Excessive application of chemical fertilizers poses a potential pollution risk to the cultivated soil layer. Applying organic fertilizer (such as livestock manure) is an economic, feasible and environmental protection way to develop sustainable agriculture. The effects of combined application of chemical fertilizer and organic fertilizer for different years on soil chemical properties and copper and zinc contents in the Yellow River irrigation area of the middle reaches of the Yellow River in Tuoketuo County of Inner Mongolia were studied, and the evolution law of soil quality under long-term combined application of organic fertilizer and chemical fertilizer was discussed. Methods The soil samples were taken from the farmland where chemical fertilizers and organic fertilizers were applied for 2-5 years. The effects of different fertilizer types and application periods on soil chemical properties and copper and zinc content were analyzed. The key parameters include pH, conductivity, water-soluble salts, cation exchange capacity, organic matter, total nitrogen, total phosphorus, available phosphorus and copper and zinc content. Results The results showed that compared with the soil with chemical fertilizer alone, the combined application of chemical fertilizer and organic fertilizer for 2-5 years significantly reduced the pH value of the cultivated layer soil in the study area by 9.33%−16.88% (p<0.05), the electrical conductivity by 35.81%−20.30% (p<0.05), the water-soluble salt content by 62.12%−55.55% (p<0.05), and the soil cation exchange capacity by 109.38%−90.61% (p<0.05), and the contents of soil organic matter, total nitrogen, total phosphorus and available phosphorus by 266.36%−491.91%, 140.79%−207.61%, 27.67%, respectively.70% to 62.94% and 561.01% to 1123.26% (p<0.05). With the increase of soil fertility, the content of heavy metals copper and zinc in soil increased significantly by 376.32% to 727.96% and 74.50% to 166.86% after 2-5 years of application of organic fertilizer, respectively (p<0.05). Conclusions Therefore, when implementing the strategy of organic fertilizer replacement and chemical fertilizer reduction, we must combine the regional soil environmental capacity and heavy metal input flux, formulate scientific and reasonable fertilization scheme, and realize the coordinated development of soil fertility and soil environmental protection.