The spatial distribution of compositional elements in milky, dough, and mature rice, together with the structure-function relationship was studied using synchrotron-FTIR. The dough stage aleurone and endosperm had high lipid, protein (amide I and II), and hemicellulose. The amylopectin chain length distribution of starch exhibited small differences among developmental stages. Dough starch featured a greater portion of A and B1 chains, implying a more crystalline and high in resistant starch. The protein in milky-to-dough stage aleurone and endosperm had higher contents of α-helixes than β-sheets, resulting in higher protein digestibility and availability. There were high intensities of the glycosidic peaks of hemicellulose and cellulose, pectin, carbohydrates, and β 1–6 glucans in milky-to-dough stages. They corresponded to higher total, insoluble, and soluble dietary fiber contents in milky-to-dough stage than in mature stage. Young-stage rice was found to be more nutritious and could thus be a functional food source.