The invention discloses a method for preparing a water-soluble fertilizer containing humic acid. The method mainly comprises the following steps: pre-treating peat, extracting humic acid from the pre-treated peat, and adding dissolved urea, monopotassium phosphate, boric acid, ammonium molybdate and microelements subjected to complexation; the water-soluble fertilizer containing humic acid, prepared withthe method provided by the invention, is complete and balanced in nutrition, good in suspension property, and convenient to apply. The results of a field trial prove that the yield of cucumbers, to which the water-soluble fertilizer containing humic acid is applied, is higher than that of a comparison group, the input-output ratio of an area, to which the water-soluble fertilizer containing humic acid is applied, is 1:9.22, and the input-output ratio of an area, to which the water and conventional fertilizer are applied, is 1:5.23.