The relationship of short-range order(SRO) minerals, their role in carbon sequestration capacity and its relation with clay carbon was studied in three soils with contrasting characteristics. The study was carried out in two phases, viz. sorghum-sudangrass depletion experiment and test crop experiment with maize using three levels of fertility status(depleted, original and fertilized with 40 ppm P and K) and two levels of rhizospheric status(rhizosphere and non-rhizosphere). After crop harvest, the clays were separated and fractionated into fine and coarse clay humus complexes and SRO minerals, total organic carbon (TOC) and labile carbon(LC) contents were estimated in them. In fine clay humus complex, mean TOC was significantly higher in Vertisol(3.01;), depleted fertility(2.96;), and rhizosphere(2.87;) samples. LC was significantly higher in depleted fertility status(1.74;), Vertisol(1.72;) and non-rhizosphere(1.82;) samples.In coarse clay humus complex, mean TOC was significantly higher in depleated fertility status(2.33;), Vertisol(2.71;) and rhizosphere(2.30;) samples, whereas for LC only significant difference was observed in soil.TOC showed significant and positive correlation with amorphous ferri-alumino silicate(AFAS) content and allophane content in fine and coarse clay humus complexes respectively. Non labile carbon showed significant positive correlation with AFAS in both the clay humus complexes and allophane content in coarse clay humus complex. Fine clay humus in any soil is most important in terms of total amount of sequestered carbon. In coarse clay humus fraction, the role of Al and Fe compound is more prominent. Alfisol is the most potential soil for sequestering carbon; rhizosphere sequesteres more carbon than non-rhizosphere.