A GWAS and identify a drought-tolerant WD40 gene TaWD40-4B.1 embedding in qDSI.4B.1 locus on chromosome 4BS of wheat. The allelic variation of TaWD40-4B.1 produces the allele TaWD40-4B.1T encoding a truncated peptide which is associated with the lower drought tolerance in the wheat accessions. The complete allele TaWD40-4B.1C enhances drought tolerance and grain yield. Intriguingly, TaWD40-4B.1C but not TaWD40-4B.1T strongly interacts with catalases, the crucial H2O2, scavenging enzymes, to promote their activity under drought stress. Thus, our research reveals that the TaWD40-4B.1 allele plays a significant role in wheat drought tolerance. Notably, we described that TaWD40-4B.1T was resulted from the allelic variation that both in either hexaploid wheat or its tetraploid progenitor, and TaWD40-4B.1T has been selected in some leading cultivars, partially because the locus containing TaWD40-4B.1T is highly linked to adjacent QTLs and genes (Rht1, etc.), which is more selected in the districts with more serious water deficiency. On the other hand, we found that TaWD40-4B.1C was an elite haplotype, which had no adverse effect on plant growth and grain yield under the well-watered condition and could be used for improving drought tolerance of the cultivar with TaWD40-4B.1T allele.