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The TaGS3 homoeologous genes (homoeologs) located on chromosomes 7A, 4A, and 7D in hexaploid wheat were cloned. Relative expression analysis of the three TaGS3 homoeologs revealed that the expression levels of TaGS3-4A and TaGS3-7D in developing grains were higher than that of TaGS3-7A. Genetic evidence showed that TaGS3 was a negative regulator of grain weight and grain size. Fifteen polymorphic sites and five haplotypes were detected in TaGS3-4A. Two molecular markers were developed to distinguish the five haplotypes. Association analysis using 260 accessions from Chinese wheat mini-core collection (MCC) indicated that TaGS3-4A affected thousand grain weight (TGW) and grain length (GL). HAP-4A-1 and HAP-4A-2 were favorable haplotypes that increased TGW and GL and had undergone strong selection during domestication of wheat. In addition, interaction of the TaGS3-4A and TaGS3-7D homoeologs had significant additive effects on the grain traits. Hap-4A-1/Hap-7D-2 was the best haplotype combination in increasing TGW and GL. The frequencies and geographic distributions of favorable TaGS3 haplotypes among 1388 wheat accessions from worldwide sources provided clues for selection of yield-related traits. Our findings demonstrated that TaGS3-4A had significant effects on TGW and GL. Marker-assisted selection of HAP-4A-1/2 combined with HAP-7D-2 has potential to increase wheat yields.