Soil organic carbon (SOC) associated with minerals is considered to be one of the most fundamental long-term SOC storage strategies, but little research has integrated the organo-mineral complexes regulated by long-term fertilization. Here, soil samples under three fertilization treatments (Control, no fertilization; NPK, chemical nitrogen, phosphorus and potassium fertilization; NPKM, NPK plus manure) from four 23–34 years long-term field experiment sites across China were examined. Chemical analyses indicated that vigorous iron (Fe) mobilization could be regulated by long-term fertilization regimes. Meanwhile, Fe K-edge X-ray absorption near-edge fine structure (XANES) demonstrated that compared to NPK treated soils, NPKM treated soils contained significantly higher concentration of poorly crystalline ferrihydrite. Results from both the Fourier transform infrared combined with two-dimensional correlation spectroscopy analyses (FTIR-2DCOS) and C 1 s X-ray photoelectron spectroscopy (XPS) revealed that aliphatic carbohydrate might play an important role in binding exogenous Fe(III) in all tested four soils. In addition, greater amounts of aromatic C (the most resistant soil C fraction) were under long-term treated NPKM than NPK soils. Furthermore, multiple regression analyses showed a significantly positive relationship between poorly crystalline Fe minerals and SOC or aromatic C. Such relationships indicated that aromatic functional groups had been attached to the poorly crystalline Fe minerals, which could also be protected from being transformed to the crystalline counterpart. In conclusion, results from our integrated spectroscopic analyses have evidenced greater improvement of both poorly crystalline Fe minerals and aromatic C in organically fertilized than in chemically fertilized soils.