Soil organic matter (SOM) and its fractions play an important role in many soil chemical, physical, and biological properties. We studied functional groups of SOM fraction using a physical and chemical fractionation scheme in long-term application of a fertilization in a rice-rice system, which started in 2005 (sandy loam). Replicated soil samples of experimental plots of four different manure and fertilizer treatments and one unfertilized control were evaluated. The unprotected coarse particulate organic matter (POM) (cPOM), pure physical protected POM (iPOM), and the biochemically silt-sized fractions (NH-dSilt) contributed the major carbon storage fractions constituting 32.16-40.37%, 13.78-23.32%, and 14.44-28.66% of the total soil organic carbon (SOC) content, respectively. Combined application of organic manure like farmyard manure along with fertilizer improved the SOC content in all unprotected, physically protected, and chemically protected, silt and clay-associated physico-biochemically, clay-associated physicochemically protected and silt-associated biochemically protected fractions compared to control. Besides, the SOC increase expressed as SOC content per unit of total SOC for iPOM, cPOM, silt associated physicochemically and physico-biochemically protected fractions (H-mu Silt and NH-mu Silt) were the highest and as large as 70%, 60%, 45%, 38%, respectively. Our study indicates that long-term addition of manure with fertilizer for a long period of soil submergence under rice cultivation promoted the formation of more stabilized pools of C through physical and chemical protection mechanism.