The invention discloses an environment-friendly fertilizer applied in the tomato seedling stage and a preparation method thereof. The environment-friendly fertilizer is prepared from the following raw materials in parts by weight: natural zeolite, 2 mol / L dilute HCl, a 6 wt% NaCl solution, ammonium chloride, a rooting agent, minor elements, a 5-10 wt% amino acid solution, fishbone dust, rice washing water, zinc sulfate, plant ash and a proper amount of water. When the fertilizer is used for planting tomatoes, the tomato seedlings have favorable growth vigor, the disease and pest incidence rate is lowered, the stress tolerance is enhanced, the fertilizer loss condition is reduced, the environment is protected, and the reduction of the direct addition of the chemical components is beneficial to environment friendliness.