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Key Message: The quantitative trait loci (QTLs) for grain morphological traits were identified via nested association mapping and validated in a natural wheat population via haplotype analysis. Grain weight, one of the three most important components of crop yield, is largely determined by grain morphological traits. Dissecting the genetic bases of grain morphology could facilitate the improvement of grain weight and yield production. In this study, four wheat recombinant inbred line populations constructed by crossing the modern variety Yanzhan 1 with three semi-wild wheat varieties (i.e., Chayazheda, Yutiandaomai, and Yunnanxiaomai from Xinjiang, Tibet, and Yunnan, respectively) and one exotic accession Hussar from Great Britain were investigated for grain weight and eight morphological traits in seven environments. Eighty-eight QTLs for all measured traits were totally identified through nested association mapping utilizing 14,643 high-quality polymorphic single nucleotide polymorphism (SNP) markers generated by 90 K SNP array. Among them, 64 (72.7%) QTLs have the most favorable alleles donated by semi-wild wheat varieties. For 14 QTL clusters affecting at least two grain morphological traits, nine QTL clusters were located in similar position with known genes/QTL, and the other five were novel. Three important novel QTLs (i.e., qTGW-1B.1, qTGW-1B.2, and qTGW-1A.1) were further validated in a natural wheat population via haplotype analysis. The favorable haplotypes for these three QTLs might be used in marker-assisted selection for the improvement of wheat yield by modifying morphological traits.