The invention discloses a method for preparing sea-buckthorn biological fodder through compound microbial flora fermentation. According to the method, compound microbial flora is adopted, and the compound microbial flora is composed of 0.5-5% of bacillus subtilis and 1-8% of beer yeast. Multi-flora coordinated fermentation sea-buckthorn fruit residues are adopted, through the coordinated transformation of different microorganisms, the bioavailability of the fruit residues is improved, so that produced sea-buckthorn biological fodder is high in disgestibility, the coarse fiber content is reduced, the protein content is substantially raised, the number of probiotics is substantially increased, the method has the advantages of being complete in nutrition, green, safe, low in cost, high in economic benefit and the like, the growth speed of beasts and birds can be remarkably enhanced, the disease-suffering rate of the beasts and birds can be lowered, the feed conversion ratio in the beast and bird culturing process is reduced, the method is applicable to large-scale and industrialization production, and the wide application and popularization prospect is achieved.