The invention relates to the technical field of veterinary drugs, and discloses a pharmaceutical composition for treating cat fatty liver as well as a preparation method and application thereof. The pharmaceutical composition is prepared from the raw materials of herba phyllanthi urinariae, clethra loosestrife herb, muskmelon base, glossy privet fruit, eucommia bark, Sinkiang arnebia root, white puncturevine caltrop fruit, common cephalanoplos herb, flower of lobed kudzuvine, giant knotweed rhizome, capillary wormwood herb, tiflawn, turmeric root-tuber, raw rhubarb, Chinese thorowax root, oriental waterplantain rhizome, pinellia tuber, cassia seed, tangerine peel, peach seed, choline chloride, and ursodesoxycholic acid according to certain weight parts. The pharmaceutical composition is simple in formula, has significant effects of clearing heat, removing fat, protecting the liver, dissipating blood stasis, excreting dampness, invigorating the spleen, promoting the circulation of qi, reducing phlegm, arresting bleeding, and soothing the liver to remove fat by virtue of organic combination, dialectic compatibility and mutual assistance, and can be used for effectively treating cat fatty liver syndromes. Clinical treatment statistics prove that the cure rate can reach 88.89%, and the effective rate is 100%. The preparation method of the pharmaceutical composition disclosed by the invention keeps active ingredients of each raw material to the maximum extent and is simple to operate, and the pharmaceutical composition does not have toxic or side effects, is easy to absorb by a diseased cat, and is suitable for industrial production.