Understanding the organomineral associations in soils is of great importance. Using two-dimensional correlation spectroscopy (2DCOS) and high resolution-transmission electron microscopy (HRTEM) techniques, this study compared the binding characteristics of organic ligands to Al(III) in dissolved organic matter (DOM) from soils under short-term (3-years) and long-term (22-years) fertilizations. Three fertilization treatments were examined: (i) no fertilization (Control), (ii) chemical nitrogen, phosphorus and potassium (NPK), and (iii) NPK plus swine manure (NPKM). Soil spectra detected by the 2DCOS Fourier transform infrared (FTIR) spectroscopy showed that fertilization modified the binding characteristics of organic ligands to Al(III) in soil DOM at both short- and long- term location sites. The CH deformations in aliphatic groups played an important role in binding to Al(III) but with minor differences among the Control, NPK and NPKM at the short-term site. While at the long-term site both C–O stretching of polysaccharides or polysaccharide-like substances and aliphatic O–H were bound to Al(III) under the Control, whereas only aliphatic O–H, and only polysaccharides and silicates, were bound to Al(III) under NPK and NPKM, respectively. Images from HRTEM demonstrated that crystalline nanominerals, composed of Fe and O, were predominant in soil DOM under NPK, while amorphous nanominerals, predominant in Al, Si, and O, were dominant in soil DOM under Control and NPKM. In conclusion, fertilization strategies, especially under long-term, could affect the binding of organic ligands to Al(III) in soil DOM, which resulted in alterations in the turnover, reactivity, and bioavailability of soil organic matter. Our results demonstrated that the FTIR-2DCOS combined with HRTEM techniques could enhance our understanding in the binding characteristics of DOM to Al(III) and the resulted nanominerals in soils.