A core set of 349 accessions from the 3K Rice Genome Project was evaluated for cooked-kernel elongation (CKE) over two years. Genome-wide association analysis identified four quantitative trait loci(qCRE1, qCRE7-1, qCRE10, and qCRE7) that accounted for 9.4% to 15.6% of the phenotypic variance. The lead SNP at qCRE7 colocalized with the previously characterized gene OsDPE2. For the three novel loci, candidate gene screening was performed by integrating functional annotations with haplotype analysis, which prioritized Os10g0162844 and Os07g0268000 as the most promising candidates. Furthermore, two accessions, IRIS_313-8656 and IRIS_313-11189 were identified as harboring favorable alleles for both grain length and CKE by aggregation analysis of different haplotypes of the candidate genes in the germplasm, offering new alleles and germplasm resources for rice quality improvement.