Abstract: Fertilization significantly alters soil chemical properties, and these changes in turn influence soil metal content and distribution. The levels and patterns of soil metals directly affect soil health, plant growth and ecosystem balance. To investigate the effects of heavy metals on the abundance of bacteria, fungi and protists in dryland red soil under different fertilization treatments, the present study was based on the long-term fertilization plot for dryland red soil at the Red Soil Research Institute in Jinxian County, Nanchang City, Jiangxi Province, and set up four treatments: no fertilization (CK), inorganic fertilizer (NPK), organic fertilizer (OM), and organic and inorganic mixed application (NPKOM). By measuring the heavy metal content and chemical properties of the soil and the abundance of bacteria, fungi and protists, and combined with the correlation analysis to reveal the key metals affecting the abundance of bacteria, fungi and protists under different fertilization treatments. The correlation analysis was used to reveal the key metal elements and their mechanisms of action that affect the abundance of bacteria, fungi and protists under different fertilization treatments. The results showed that: compared to no fertilization (CK), organic fertilizer (OM) and organic-inorganic (NPKOM) treatments significantly increased the abundance of bacteria, fungi, and protists, whereas the inorganic fertilizer (NPK) treatment only increased the abundance of bacteria and fungi and had no significant effect on the abundance of protists. In addition, compared to no fertilization (CK), the organic fertilizer (OM) and organic-inorganic (NPKOM) treatments significantly increased the content of Mg and Ca elements in the soil, while decreased the content of Al and Fe. Further correlation analysis revealed that the abundance of protists was significantly positively correlated with soil pH, organic carbon, total phosphorus, Mg and Ca content, and negatively correlated with soil Al and Fe content. Further correlation analysis revealed that the abundance of bacteria, fungi and protists was significantly positively correlated with soil total phosphorus, total nitrogen, organic matter, available potassium, available phosphorus, dissolved organic carbon, nitrate nitrogen and ammonium nitrogen. Simultaneously, the abundance of bacteria and protists showed significant positive correlations with soil Mg and Ca content, while exhibiting significant negative correlations with soil Al and Fe content. This difference can be attributed to the fact that organic fertilizer additions may reduce the Al and Fe content by inducing the formation of organic iron aluminum composite, providing more habitats and nutrient supply for microorganisms, which in turn promotes the abundance of bacteria, fungi and protist; whereas organic fertilizer additions indirectly increased the metabolic efficiency and surface attachment sites of microorganisms by increasing the Ca and Mg content, which ultimately led to an increase in the abundance of bacteria, fungi and protist. In conclusion, In conclusion, the application of organic fertilizers can increase the abundance of bacteria, fungi and protist by decreasing the content of Al and Fe, and increasing the content of Mg and Ca. The results of this study can provide an important theoretical basis for optimizing the fertilization strategy of dryland red soil and elucidate the response mechanisms of soil microorganisms to metal elements.