Grain shape is an important appearance quality trait that is associated with grain weight in rice. Dissection of the genetic basis of grain shape will benefit the improvement of grain shape. In this study, we constructed a high-density genetic linkage map via genotyping a recombinant inbred line population by a single nucleotide polymorphism (SNP) array. A total of 22 quantitative trait loci (QTLs) were detected, one half was detected in both years of the experiment, and the other half only in one year. As well as the QTLs reported in previous studies, five novel QTLs were identified, which could be targets for marker-aided selection for grain shape improvement. Six pleiotropic QTLs were identified and well explained the correlations among traits. Complementary action of additive QTLs adequately accounted for the genetic basis of transgressive segregation. One to six heterogeneous inbred families for all detected QTLs were searched in the recombinant inbred population, which provided a good chance to quickly produce near isogenic lines. These new QTLs could be quickly validated and fine mapped on the basis of these HIFs.