The invention discloses a pantoea agglomerans strain and application thereof. The pantoea agglomerans strain is named as Pantoea agglomerans ZJU23, with a preservation number of CGMCC No.16174 and a preservation date of July 30, 2018. According to the pantoea agglomerans strain, the control effect on wheat scab is up to 50-70%, vomitoxin is reduced by 50-80%, diseases caused by plant pathogenic fungi such as gibberellic disease, gray mold, rice blast, colletotrichum destructivum and rice sheath blight disease can also be simultaneously controlled, and the range of controlling is wide.