The invention provides a microbial agent used for removing DDT on the surfaces of fruit and vegetable and a preparation method thereof. The microbial agent comprises, by weight, 10 to 20 parts of xylose, 10 to 30 parts of trehalose, 10 to 20 parts of glucose, 3 to 10 parts of yeast extract, 10 to 15 parts of lactose, 30 to 50 parts of plant extract, 6 to 8 parts of Bacillus spp., 5 to 8 parts of Pseudomonas, 3 to 5 parts of Tween-80, 2 to 5 parts of iron chloride and 700 to 2500 parts of water. The microbial agent is green, environment friendly, purely natural and free of pollution and does not produce poisonous and harmful substances in the process of removal of DDT.