We aimed to understand the genetic basis of nonstructural carbohydrate(NSC) accumulation and translocation in rice culms and leaf sheaths. Quantitative trait loci (QTL) for 5 related traits were mapped with use of a recombinant inbred line derived from a cross between Lemont (japonica var.) and Teqing (indica var.) under direct sowing. Three QTL affecting NSC content at heading and maturity were detected on chromosomes 1, 9 and 12, explaining 13%, 7% and 7%, respectively, of the phenotypic variation. The Teqing alleles increased the trait value at all three QTL. Two QTL for NSC translocation rate were identified on chromosome 12 and accounted for 8% and 14%, respectively, of the total variation.The number of QTL for seed-setting rate and 1000-grain weight were 3 and 4, respectively. The amount of variation explained by the seed-setting rate QTL were 9%, 24% and 6%, and that explained by the 1000-grain weight QTL were 14%, 11%, 12% and 13%. The Lemont allele decreased NSC content at maturity but increased NSC translocation rate, seed-setting rate and 1000-grain weight at the region near RM277 on chromosome 12. The Teqing allele increased both NSC translocation rate and seed-setting rate at the region near OSR20 on chromosome 12, which provides a genetic explanation for the close correlations among the traits.