The invention belongs to the field of agricultural thin films and discloses herbicide master batch as well as a preparation method and application thereof. The herbicide master batch comprises the following components by mass percentage: 25%-75% of PE (Poly Ethylene) resin, 10%-60% of a herbicide and 2%-15% of a modifying agent. The herbicide master batch provided by the invention adopts the modifying agents including an ethylene-vinyl alcohol copolymer and an ethylene-acrylic copolymer and the like to pre-treat the herbicide; in the processing process, the modifying agents are fused and then are coated on the surface of the herbicide so as to form a core-shell structure which takes the herbicide as a core and takes the modifying agents as the shell, effectively protect the herbicide and reduce the loss caused by thermal decomposition of the herbicide at a high temperature in a preparation process of the herbicide master batch and a mulching film. The herbicide master batch provided by the invention is used for preparing the weeding mulching film; the herbicide master batch is dispersed uniformly, the releasing speed of the herbicide is slowed, the pesticide effect time can be prolonged, and the weeding effect can still be up to be more than 90% after the mulching film covers for 60 days.