The crease region (CR) is the most characteristic external morphological feature of wheat, and its shape and depth are important indicators for evaluating the quality of wheat grains. However, the genetic architecture of the crease region of wheat is still not clear. In this study, we re-sequenced 413 wheat accessions and developed a method for evaluating the phenotypic data of CR. CR trait exhibited continuous and significant broad variation in the natural population, and the broad-sense heritability reached 84.09%. Correlation analysis showed that CR was positively correlated with yield-related traits and negatively correlated with quality-related traits. Analysis of traits differentiation between landraces and cultivars showed that yield-related traits and CR were continuously improved during breeding improvement. Moreover, a total of 989.7Mb genetic segments were identified that fell within the selective sweeps between landraces and cultivars, which contained some known functional genes for quality and yield-related traits. Subsequently, 186 significant SNPs and 18 QTLs were detected significantly associated with CR by genome-wide association study (GWAS). In all, 1,757 genes were found in those QTLs. Among them, several genes related to grain development and located within the selection regions were selected as candidate genes for further analysis. To our knowledge, this is the first time to provide a genetic basis for crease region during breeding improvement and those genetic loci identified in this study may ultimately assist in overcoming the trade-off between yield and quality in wheat.