The invention discloses a compound microbial fish fertilizer special for silver carp and a preparation method thereof. The compound microbial fish fertilizer special for silver carp comprises the following components in parts by weight: 0.5-0.8 part of silicate bacteria, 1-3 parts of streptococcus faecalis, 0.6-0.8 part of trichoderma sp, 2-5 parts of rhodopseudomonas palustris, 0.3-0.5 part of saccharomycetes, 50-60 parts of fishbone dust, 65-70 parts of vinegar residue powder, 50-55 parts of effluent precipitate, 40-60 parts of rice bran, 12-14 parts of brown sugar, 10-14 parts of table salt, 80-85 parts of pig manure, 45-55 parts of waste of a pig meat slaughter house, 60-65 parts of aquatic plants, 12-16 parts of calcium bicarbonate, 14-17 parts of urea, 1-3 parts of ferric citrate, 0.6-0.8 part of vitamin B1, 0.2-0.6 part of Vitamin B12, 1-3 parts of rheum officinale, 2-6 parts of Astragalus membranaceus and 4-7 parts of medicated leaven. The fertilizer disclosed by the invention can promote silver carp to grow quickly, the EPA content of fish is increased, the fish diseases are reduced, and the number of dead fish is reduced, and meanwhile, beneficial microorganisms in water are increased. Finally, both the quality and the weight of silver carp are improved.