The invention belongs to the application of prevention and treatment of plant diseases and in particular relates to a chitosan oligosaccharide-iodine complex as well as a preparation method and application thereof. In the complex provided by the invention, the mass ratio of chitosan oligosaccharide to iodine ranges from (10 to 2) to (2 to 1); the average molecular weight of the chitosan oligosaccharide is 1000Da to 5000Da and the deacetylation degrees is more than or equal to 90%. A complexing process of the chitosan oligosaccharide-iodine complex is finished in specific equipment at certain temperature in a reaction medium after certain time; the appearance of the liquid chitosan oligosaccharide-iodine complex is liquid which is deep brown to black and has a slight pungent smell; the solid is yellowish-brown and the pH value is 4 to 6. The chitosan oligosaccharide-iodine complex has good bacteria-inhibiting and sterilization effects on a plurality of pathogenic microorganisms including colon bacillus, salmonella, staphylococcus aureus, rice sheath blight pathogenic bacteria, apple rot pathogenic bacteria and cotton wilt pathogenic bacteria under an effective concentration thereof. The chitosan oligosaccharide-iodine complex has a remarkable growth promotion effect on plants.