The present application discloses a semi-dominant molecular marker related to maize dwarf and an application thereof, and relates to the technical field of maize molecular breeding. The molecular marker related to the maize dwarf is caused by a non-synonymous mutation from G to A in a maize gene Zm00001d013465, and the molecular marker is a nucleotide sequence composed of the non-synonymous mutation site and its upstream and downstream bases. The present application identifies a dwarf mutant, coded as E5779, from an EMS mutation population with maize B73 as the genetic background. By genome resequencing and Mutmap mapping, it is found that the mutant is caused by the non-synonymous mutation from G to A in the gene Zm00001d013465. The molecular marker is developed based on this, and the analysis and utilization of E5779 are helpful to improve the maize plant height and density-tolerant breeding, it has an important breeding application potential.