Soil acidification is a natural process, and it is well known that soil acidification can be accelerated by long-term fertilization (LTF). Nevertheless, how this acidification occurs and how the mineralogies of iron oxides as the important active clay components in red soil respond to the acidification is still less understood. In this study, soil samples from 23 years (1990–2013) of long-term fertilization experiments were collected from the Qiyang Red Soil Experimental Station in southern China. The physicochemical properties of the soil samples were analyzed. A significant negative linear correlation between soil pH and log(Al_py) (complex-state aluminum) as well as log(Al_exch) (exchangeable Al³⁺) illustrate that Al_py and Al_exch are the most sensitive species to soil acidification compared with the other factors. In addition, the mineralogical characteristics of the iron oxides in five typical LTF treatments, including the control, chemical fertilizer N, NPK, NPK plus manure and manure were analyzed using the synchrotron differential XRD patterns (DXRD). The results obtained revealed that the LTF treatment with chemical N reduced the total content of iron oxides and the ratio of goethite to hematite (G/H value), and the transformation of iron oxides and accumulation of hematite in the soil would reduce the soil's buffering capacities to acidification. In contrast, the LTF treatments with manure (NPKM and M) presented the opposite trends. In addition, a positive relationship between soil pH and the IOs_Almol% (isomorphous substitution ratio of Al for Fe in iron oxides) was also found. Therefore, the potential acid Al³⁺ ions in soil are reduced through the ionic substitution of Al for Fe in the structure, which may further mitigate the process of soil acidification. These results provide new insights for further understanding the soil acidification processes induced by LTF and how those iron oxides respond to soil pH during soil acidification.