The reduction of chemical fertilizers is a management practice gradually being adopted in long-term fertilized soils. However, the effects of chemical fertilizer reduction on soil health have remained underexplored in orchard systems. Through a two-year field experiment, we investigated how the reduction of chemical fertilizers affects soil chemical properties, the soil quality index (SQI), and fruit yield and quality. The results indicated that chemical fertilizer reduction significantly increased soil pH and organic matter, while it decreased the available nitrogen and phosphorus contents in 2022 and 2023. The reduction of chemical P fertilizer enhanced the availability of Si, S, Mn, and Cu, while it had no impact on the availability of Mo, Fe, and B. Chemical fertilization reduction did not decrease fruit yield and quality, except for the 1/3N treatment. Moreover, the SQI for the N and 2/3N treatments was higher. The random forest model demonstrated that SQI and soil pH were the most important driving factors regulating fruit yield in response to chemical fertilizer reduction practices. Our study suggests that the appropriate reduction of chemical fertilizers can enhance SQI and the availability of micronutrients without decreasing fruit yield and quality, which may have direct implications for soil health.