Abstract: The disclosure belongs to the technical field of functional molecular marker, and discloses a molecular marker of maize ear rot resistance, gene and use thereof. In the disclosure a major gene zmSRR1 of maize ear rot resistance is cloned, and the gene's resistance to Fusarium verticillioides is checked by transgenic method. By comparing sequences and a candidate gene association analysis combined with resistance phenotypes, three natural variation sites affecting maize ear rot resistance are confirmed, and are found to be combined into five haplotypes in natural materials. Among which one is a high ear rot susceptible haplotype, so that the steps of detecting variation sites, confirming haplotypes, identifying types of resistance genes in maize, confirming whether disease resistance improvement can be targeted, tracking and monitoring the subsequent breeding are conducted.