The invention discloses a Bacillus amyloliquefaciens strain and application thereof. The strain is Bacillus amyloliquefaciens ZTS-06, and the collection number is CGMCC No.11165. The invention also discloses a live strain preparation containing the strain and a preparation method thereof. The live strain preparation is prepared by the following steps: carrying out amplification culture on the Bacillus amyloliquefaciens ZTS-06, inoculating in a fermentation culture medium, culturing to obtain a fermentation liquid, adding propyl gallate, beta-cyclodextrin and soluble starch, and carrying out spray drying to obtain live strain raw powder; and adding abundant soluble starch, and uniformly mixing to obtain the live strain preparation. The strain has favorable degradation effects on phenylallyl propionic acid, para-hydroxybenzoic acid, cinnamic acid and the like, and can relieve succession cropping obstacles caused by phenolic acid and other toxic substances. The living strain preparation has the advantages of short fermentation period, high fermentation liquid bacterium concentration, low live strain loss in the spray drying process, and high stability in the storage process.