Wheat660K, the Affymetrix® Axiom® Wheat660, was designed by the Chinese Academy of Agricultural Sciences and synthesized by Affymetrix. This Wheat660K SNP array is genome-specific with high density and is highly efficient with a wide range of potential applications (http://wheat.pw.usda.gov/ggpages/topics/Wheat660_SNP_array_developed_by_CAAS.pdf). However, genetic position in relation to Wheat660K SNPs has not yet been documented. In this work, for the first time, we report a high-density map for wheat constructed from this Wheat660K SNP Array. Based on SNP flanking sequences, we assigned SNPs to the genome assembly of T. aestivum cv. Chinese Spring (CS) (https://urgi.versailles.inra.fr/download/iwgsc/IWGSC-WGA_Sequences/). We also compared our high-density genetic map with the consensus genetic maps of Wheat90K and Wheat820K based on the common contigs assembled in the chromosome survey sequencing (CSS) project. Comparative genomic analyses based on the mapped SNP flanking sequences and the corresponding contig sequences were also performed with the genomes of Brachypodium distachyon, Oryza sativa, Zea mays, and Sorghum bicolor. Using this mapping resource along with the phenotypic data, we identified important QTLs for yield-related trait. A major stable QTL for kernel number was identified and then characterized in detail based on the high-density genetic map and comparative genomic analysis.