【Objective】In this study, the synchrotron radiation infrared micro-imaging method was used to characterize mineral-organic complex in soil microaggregates of the red soils under long-term application of organic manure or chemical fertilizer in the long-term stationary experiment station of the national soil fertility network in Qiyang, Hunan, China. 【Method】Soil samples were collected from the long-term experiment station for fractionation of soil microaggregates using the dry sieving method. The obtained soil microaggregates were spread over on a Whatman GF/A Filter, mounted onto a sieve and fixed to a chimney funnel that transferred warm mist from a humidifier filled with ultrapure water. Excess droplets on the filter were drained. Then the soil microaggregates were frozen at -20 ℃ and directly cut into thin sections (300~600 nm) on an ultramicrotome using a diamond knife. Sections were transferred to infrared-reflecting MirrIR Low-E microscope Slides. 【Result】Results show that clay minerals (3 620 cm^-1) and larger molecular organics (i.e., lipids, 2 920 cm^-1; proteins, 1 650 cm^-1; and polysaccharides, 1 080 cm^-1) were distributed in a pattern highly heterogeneous. However, among them clay minerals and polysaccharides were quite similar in distribution pattern, but differed sharply from lipids and proteins. Compared to the soil under long-term chemical fertilization, the soil under long-term application of organic manure had clay minerals and larger molecular organics distributed in soil microaggregates with higher dispersivity. Furthermore, in terms of determination coefficient (R²) with clay minerals, the organic functional groups followed an order of lipid > polysaccharide > protein in both soils, suggesting that affinity of clay minerals with larger molecular organics varied in soil microaggregates, and was not affected by fertilization of either chemical or organic. Meanwhile, the synchrotron radiation microzone infrared spectra further demonstrated that characteristic peaks of both clay minerals and larger molecular organics increased in intensity from the outer to the inner of the soil microaggregates. 【Conclusion】In summary, the synchrotron radiation infrared micro-imaging method provides a novel research means and useful information to the study on characterization of mineral-organic complexes in soil microaggregates.