A doubled-haploid population, consisting of 81 DH lines derived from the F1 hybrid of a cross between an indica cultivar and a japonica cultivar, was used to map quantitative trait loci (QTL) controlling numbers of vascular bundles in peduncle, primary rachis branches and the ratio of vascular bundles to primary rachis branches (V/R ratio). For vascular bundles, three QTL were detected. Among them, the QTL qVB-8 with the largest effect individually accounted for 31.1% of the total variation. Two QTL controlling primary rachis branches were identified and they were co-located with 2 of the 3 QTL for vascular bundles respectively. Three QTL for the V/R ratio were mapped on chromosome 1, 2 and 8, respectively. Of the three QTL, the QTL qV/R-1 with the largest additive effect, explained 25.3% of the total variation, was located on chromosome 1 and found to be closely linked to the gene sh-2, a major gene underlying grain-shattering ability. In addition, four and two pairs of significant epistatic QTL were detected for vascular bundles and the V/R ratio, respectively, but none for rachis branches. Our results suggested that the numbers of vascular bundles and primary rachis branches were independently controlled by different polygenic systems, but the two polygenic systems shared a fraction of quantitative trait loci. It was also shown that the chromosome region carrying the QTL qV/R-1 on chromosome 1 might play an important role in the processes of indica-japonica differentiation in rice.