The invention belongs to the field of fertilizers, and particularly relates to a modified seaweed functional water-soluble fertilizer and a preparation method thereof. The fertilizer comprises the following components: 8-51% of a nitrogen fertilizer, 8-40% of a phosphorus fertilizer, 20-78% of a potassium fertilizer, 0.1-0.2% of a trace element fertilizer, 2-4% of seaweed, 0.1-0.2% of an AT modifier, and 0.1-0.2% of a stabilizer, wherein the AT modifier is prepared by compounding organic acids and alkylphenol ethoxylates. According to the invention, a scheme of mixing alkaline seaweed with macroelements, medium elements and trace elements is adopted, so that the problem of acid-base mixing between seaweed and a macroelement water-soluble fertilizer is solved, organic nutrients and inorganic nutrients are combined, the growth of crops can be activated during fertilization, the growth vigor of the crops is improved, and the quality and yield of the crops are improved; meanwhile, the organic nutrients also have an improvement effect on the soil, and rich absorbable organic nutrients are provided, so that the seaweed and the macroelement, medium element and microelement water-soluble fertilizers have a mutual synergistic effect.