We studied the storage of sucrose, starch, and hexose before heading in rice (Oryza sativa L.) plants by quantitative trait locus (QTL) analysis with a population of backcross inbred lines (BILs) of japonica cv. Nipponbare x indica cv. Kasalath. Carbohydrates are accumulated in the rice plant before heading and are translated to the panicle after heading. A higher capacity for accumulation is thus a main target for improvement in yield. The form of carbohydrate (sucrose, starch, or hexose) differs depending on the organ in which it is stored. There was no correlation between starch and sucrose or hexose contents in BILs, and the positions of QTLs controlling starch differed from those for sucrose and hexose accumulation. These results suggest that the genetic control of accumulation differs between starch and sugars. QTLs that control the ratio of sucrose to starch content were detected, suggesting the existence of a mechanism(s) that determines this ratio. On chromosome 1, sucrose-phosphate synthase 1, the key enzyme in sucrose synthesis was close to the peaks of the likelihood odds ratios in QTLs for sucrose or hexose content. These results suggest that SPS1 is related to conversion of carbohydrate to sucrose as accumulated form in a plant before heading.