Wheat is one of the staple food crops. Grain yield (GY) improvement is a priority for wheat breeding in the scenario of climate change and population growth. WRKY transcription factors are multifaceted regulators in plant growth, development, and response to environmental stimuli. Currently, WRKY gene TaGSNE (Grain Size and Number Enhancer) has been cloned in common wheat. It has relatively high expressions in leaves and roots, and is induced by multiple abiotic stresses. Eleven single nucleotide polymorphisms were identified in TaGSNE, forming two haplotypes in multiple germplasm collections, i.e. TaGSNE-Hap-1 and TaGSNE-Hap-2. Of them later was significantly associated with higher spikelet number per spike (SNPS; 4.13%) and thousand grain weight (TGW; 3.00%) in multiple environments, and deeper roots (10.1%) and higher root dry weight (8.3%) at mid-grain filling stage, which were verified in backcross introgression populations. Furthermore, the rice lines overexpressing TaGSNE had larger panicle, more grains, bigger grain size and higher GY relative to the non-transgenic control. Geographic and temporal distributions revealed that TaGSNE-Hap-2 is positively selected in China and Pakistan, and TaGSNE-Hap-1 in Europe. Our findings demonstrate that TaGSNE overcomes the tradeoff between TGW/grain size and grain number, leading us to conclude that the elite haplotype and functional markers may be utilized in marker assisted selection for high-yield breeding.