Abstract: Fertilization can cause significant alterations in the chemical properties of soil, with these changes in turn influencing soil metal content and distribution. Moreover, the levels and patterns of these metals can have a direct influence on soil health, plant growth, and ecosystem balance. In this study, performed at the Red Soil Research Institute in Jinxian County, Nanchang City, Jiangxi Province, we investigated the effects of heavy metals on the abundances of bacteria, fungi, and protists in a long-term fertilization plot for dryland red soil, in which we set up the following four treatments: no fertilization, application of chemical fertilizer, application of organic fertilizer, and combined application of chemical and organic fertilizers. By measuring the chemical properties and the contents of heavy metals in soil and the abundances of bacteria, fungi and protists, and performing correlation analysis, we sought to identify the key metals influencing the abundance of these organisms under different fertilization treatments, and the associated mechanisms of action. The results revealed that compared with no fertilization, organic fertilizer and combined chemical and organic fertilizer treatments significantly increased the abundances of bacteria, fungi, and protists, whereas the chemical fertilizer treatment only increased the abundances of bacteria and fungi, it had no significant effects on that of protists. In addition, compared with no fertilization, the organic fertilizer and combined chemical and organic fertilizer treatments significantly increased the contents of Mg and Ca elements in the soil, while reduced the contents of Al and Fe. Further correlation analysis revealed that the abundance of protists was significantly positively correlated with soil pH, and contents of organic carbon, total phosphorus, and Mg and Ca, and negatively correlated with soil Al and Fe contents. Correlation analysis also revealed that the abundances of bacteria, fungi, and protists were significantly positively correlated with soil total phosphorus, total nitrogen, organic matter, available potassium, available phosphorus, dissolved organic carbon, nitrate nitrogen, and ammonium nitrogen contents. Our findings indicated that the abundances of bacteria and protists were significantly positively correlated with soil Mg and Ca contents. However, their abundances were significantly negatively correlated with soil Al and Fe contents, which could be attributed to the fact that the addition of organic fertilizer may cause reductions in the Al and Fe contents of soil by inducing the formation of organic iron-aluminum composites. This would accordingly provide a greater range of habitats and more abundant nutrient supply for microorganisms, which in turn would promote increases in the abundances of bacteria, fungi and protists, whereas by promoting increases in the contents of Ca and Mg. The addition of organic fertilizer may indirectly enhance the metabolic efficiency and surface attachment sites of microorganisms, ultimately leading to increases in the abundances of bacteria, fungi, and protists. In conclusion, by contributing to reductions in the contents of Al and Fe, and increasing the contents of Mg and Ca, the application of organic fertilizers can increase the abundances of bacteria, fungi and protists. Our findings in this study provides an important theoretical basis for optimizing fertilization strategies for dryland red soil and contribute to elucidating the response mechanisms of soil microorganisms to metal elements.