The invention provides a rice kernel smut fungus effector gene Smut_5844 and application thereof. The nucleotide sequence of the gene is shown as SEQ ID NO:1; and the amino acid sequence of a proteincoded by the gene is shown as SEQ ID NO:2. By cloning the rice kernel smut fungus effector gene and analyzing the function, a pesticide molecular target can be designed; the receptor protein gene of the effector protein in host cells of rice and the like can also be knocked out or mutated to obtain a persistently disease-resistant variety; the invention can help establish a molecular assay systemfor the pathogenic mutation of the natural population of smut fungi, the distribution of the smut fungus effector gene in the field natural population is studied, and the composition and mutation characteristics of microspecies in the smut fungus population are disclosed; and the invention also contributes to the evaluation of the disease resistance of rice varieties and variety distribution and rotation, so that the occurrence of rice kernel smut fungui can be effectively controlled.