The invention relates to the technical field of water culture fertilizer, and specially relates to a preparation method of a water culture fertilizer for hydroponic crops. According to the preparation method, in a coating machine, an alginate water solution is used to carry out a coating treatment, then a crosslinking agent water solution is adopted to carry out a wrapping treatment to prepare dry particles; then an epiboly agent is added to carry out an epiboly treatment; after the alginate water solution reacts with the crosslinking agent water solution and the epiboly agent; the sustained-release period is prolonged, the water culture environment is improved; furthermore, as the sustained-release period is prolonged continuously, the alginate macromolecules are degraded into micromolecules, the fertilizer in the wrapped layer is completely released; after the sodium citrate in fertilizer particles is released, the alginate gel can be dissolved quickly, the alginate gel is decomposed, and the quality of water culture nutrient solution is improved.