<p>Grain quality of rice (<i>Oryza sativa L.</i>) holds significant cultural value for Northeast Asian consumers, with low levels of amylose and protein content preferred for their contribution to the soft and sticky texture of cooked rice. Understanding the genetic diversity at the subpopulation level, in conjunction with local adaptation as identified by the signatures of selection for amylose and protein content, forms the basis for precise calibration of phenotypes in local breeding programs. This study investigated the genetic and phenotypic variations, as well as selective sweeps for amylose and protein content, in rice accessions from China, Japan, and Korea to reveal how their genomic landscapes have been shaped. The Northeast Asian rice accessions were identified as temperate <i>japonica</i> with distinct country-specific population structures. Phenotypic analysis revealed overlapping but distinct distributions of amylose and protein contents, with the Japanese panel exhibiting the lowest mean protein content, the Korean panel showing narrower trait distributions reflecting uniform selection, and the Chinese panel displaying broader variations. Genome-wide scans identified loci under selection for low amylose and protein contents, with major peaks on chromosomes 3, 6, 10, and 11 shared across countries, suggesting conserved loci critical for grain quality improvement. Country-specific selection signals, such as <i>OsAGPS2</i> on chromosome 8 in Japan, chromosome 6 in Korea, and <i>OsAAP11</i> on the short arm of chromosome 11 in China, highlight local adaptation and breeding strategies. These findings provide valuable insights into the genetic architecture of grain quality traits and suggest candidate loci for applications in marker-assisted selection or genome editing. By addressing both regional preferences and shared targets, this study lays the foundation for developing rice cultivars that align with consumer demands while promoting agricultural sustainability and food security.</p>