The invention discloses a special biological fish fertilizer and a preparation method for the fertilizer used in aquiculture; wherein, the biological fish fertilizer mainly comprises raw materials as follows: microbiological preparation, inorganic fertilizers, fermentation organics, micro-mineral amino acid chelate, mineral composites, and water quality improver. The preparation method for the special biological fish fertilizer in aquiculture comprises steps as follows: microbiological preparation is produced; fermentation organics is then produced, and the micro-mineral amino acid chelate is produced, eventually the finished products are made. The special biological fish fertilizer has the advantages of limiting the growth and reproduction of the harmful algae, promoting the large-scale growth and reproduction of the suitable food for fish, effectively improving the water quality and purifying the water environment, strengthening the fish immunity, reducing the diseases, reducing cost due to the small use level, convenient use, mild odor, no pollution to the water, and environment protection. By combining the modern bioengineering technique, low-temperature drying technique, spray-drying technique, and super-fine crushing techniques, the preparation method has the advantages of stable quality for the fish fertilizers and lower overall cost.