High-density Wheat 660K and 90K SNP arrays are powerful tools for understanding the genetic basis of wheat traits; however, their physical positions are not very precise since they were predicted based on different versions of the Chinese Spring genome. Here, we updated positions of each SNP of these two arrays based on the AK58 genome, the most complete hexaploid wheat genome database at present, and found that  92.3% and 83% of SNPs in the respective Wheat 660K and 90K SNP arrays were precisely mapped to the AK58 genome. These updated arrays were applied to the genome-wide association studies of dough rheological properties of Chinese bread wheat, and the results indicated that 26 significant intervals composed of 1032 SNPs were associated with 9 quality traits in multiple environments over 4 years. Before being updated, the significant interval for stability time on 1D was 407875297-416222857 bp based on the 660K array and 1011346-2290849 bp based on the 90K array in two populations, and their distance was  405 Mb. After being updated, their positions were 410958209-419370971 bp and 410958467-436196126 bp, respectively, with an 8.4-Mb region overlapped. Linkage analysis indicated that the QST.henau-1D.2 for stability time was detected within the overlapped interval and could narrow to 1.64 Mb. Haplotype analysis indicated that this interval increased stability time by an average of 3.1 min. Collinearity analysis identified 9 annotated genes in this interval. A change in the physical position of multiple intervals showed the need to update the Wheat 660K and 90K arrays.