The invention discloses an aquatic animal medicine feeding capsule and a preparation method thereof. The preparation method comprises the following steps of: uniformly mixing medicines to be fed and fish feeds, subsequently packaging the mixture into gastric-soluble hollow capsules to form medicine capsules, further covering a layer of agar on the surfaces of the medicine capsules, and spraying a layer of dimethyl-beta-dimethylpropiothetin (DMPT) on the surface of the agar, and airing to obtain the aquatic animal medicine feeding capsules. The aquatic animal medicine feeding capsule disclosed by the invention can be directly swallowed by fishes, so that experimental steps of ordinary drenching and the like are avoided, stress harm and operation harm to fishes are reduced, the phenomenon of return vomit is reduced, and the quantitative feeding of the medicines can be accurately carried out.