The invention relates to the field of molecular biology and genome breeding, and particularly discloses a corn whole genome SNP chip and application thereof. SNP loci covering a genetic expression area and SNP loci which are uniformly distributed in the whole genome are collected, after sifting, a high-throughput Infinium SNP chip of Illumina is prepared, and the chip comprises 500 probes of SNP markers shown in a detection list 1. By means of the selected SNP loci based on a large-scale sequencing result, specific signals which have reasonable frequency distribution, a low miss rate and low false positives are obtained, wherein 2/3 SNP loci are distributed in all the corn warm zone and tropical zone materials, and can be effectively used for selecting and utilizing the tropical zone materials; 426 SNP loci are functional markers, and are obviously relevant to kernel substance accumulation gene expression; an Infinium platform of Illumina has the advantages of being high in SNP typingdetection rate, high in repetitive rate, simple in detection and high in accuracy. The corn whole genome SNP chip can be used for corn germplasm resource molecular marker fingerprint analysis, corn linkage map construction, QTL locating, corn breeding material background selection and the like.