Abstract: The present disclosure provides a genome-wide maize SNP array and use thereof. In the present disclosure, by means of large-scale sequencing mining, aiming at the problems of the existing high-density arrays of maize, 400 broadly representative maize inbred lines inside and outside of China are deeply sequenced to mine excellent loci therefrom, and research results of six maize arrays are integrated; by adopting the steps of biological information data analysis, locus basic parameter evaluation, probe design evaluation, a set of SNP locus combination, containing 1,536 loci, is formed, and genotyping is realized on an Affymetrix axiom platform. The genome-wide maize SNP array of the present disclosure contains probes for the 1,536 SNP loci. The array of the present disclosure can be used in DNA fingerprint construction, cultivar identification and confirmation of maize cultivars, research on germplasm resources at a genomic level, and molecular marker-assisted selective breeding.