Wheat grain morphology is an important breeding target due to its impact on yield and end-use properties. However, the genetic basis of grain roundness, which is a major determinant of grain morphology, remains largely unexplored. In this study, F₂ and recombinant inbred line (RIL) populations from a Zhongkemai 138 (ZKM138)×Chinese Spring (CS) cross were employed to analyze the genetic basis of grain shape variation. Kompetitive allele specific PCR (KASP) markers were developed according to single nucleotide polymorphisms (SNPs) from bulked segregant exome sequencing (BSE-Seq) of F₂ and Wheat 55K SNP array data online. Those SNPs were then used to construct two genetic maps of the F₂ and RIL populations, spanning 148.89 cM (30 KASP markers) and 129.82 cM (25 KASP markers), respectively. Using the traditional QTL mapping method based on these two maps, a stable quantitative trait locus (QTL) for grain roundness (GR), QGr.cib-5A, could be repeatedly detected in the interval of 444.8–455.5 Mb on chromosome 5A. Further conditional QTL mapping analysis revealed that grain width was the major contributor to GR at this locus. In addition, the use of two tightly linked markers, 5A4-15 and 55k-31, showed a 96.27% transmissibility of ZKM138-derived alleles in 134 ZKM138 derivatives, along with a 7.38% increase in GR and a 65.19% distribution among worldwide varieties. Finally, TraesCS5A02G236400, which may encode a hydroxyproline-rich glycoprotein family protein, was deduced to be the candidate gene. Collectively, these results can facilitate wheat grain shape improvement and enhance the market value of wheat.