Grain size is a major component of rice grain yield and grain quality.Here we conducted genetic analysis for grain size using an F8 recombinant inbred lines (RILs) population derived from the cross between two elite indica parents, the slender-grain line Taifeng B (TFB) with good grain quality and the high-yielding short-grain cultivar Tesanai 2 (TSA2).Strong positive association between hundred-grain weight and grain width was observed, but significant negative correlation was found between grain length and grain width.A total of 31 QTLs for grain weight, grain length, grain width, grain length/width ratio and grain thickness were identified and they explained a total phenotypic variance ranging from 51.4% to 73.8%.Of them, 9 QTLs were reported for the first time and they are likely novel genetic loci.Moreover, QTLs for grain size tend to form clusters at similar locations.Three of them were detected on chromosome 3, 5, and 7, locating at the regions of the previously reported loci GS3, qSW5/GW5 and GS7, respectively.The allele variance of the above three loci between the parental lines was verified by using functional marker and genome re-sequencing.The major QTLs and QTL clusters discovered in this study are valuable for improvement of rice grain yield and quality through marker-assisted selection (MAS).The repeatedly detected QTLs and newly identified loci provide foundation for further fine mapping and map-based cloning.