The invention discloses a special amino acid fertilizer-water paste for aquiculture and a preparation method thereof. The special amino acid fertilizer-water paste for aquiculture is prepared from the following raw materials in certain proportion: an amino acid solution, microelements, fermentation organic substances, inorganic fertilizers, minerals, a water quality improver, beneficial bacteria and a thickening agent. The preparation method comprises the following steps: A. production of amino acid solution namely, a. hydrolyzing; b. neutralizing; c. filtering; d. concentrating; B. production of fermentation organic substances: a. mixing: evenly mixing organic raw materials with the amino acid solution; b. inoculation: evenly mixing the organic raw materials with beneficial bacteria; c. fermentation; and C. production of amino acid fertilizer-water paste: a. chelation: heating the amino acid solution, adding microelements while stirring to perform chelation; b. mixing: sequentially adding the fermentation organic substances, inorganic fertilizer, minerals, water quality improver and beneficial bacteria, and evenly mixing; c. thickening: adding a thickening agent, and evenly mixing; d. inspection. The invention enhances the immunity of fish, reduces the occurrence of diseases, increases the culture yield of bighead, lowers the fish culture cost, and improves the fish quality.