The invention discloses a composite seaweed fertilizer and a preparation method thereof. The composite seaweed fertilizer comprises raw materials and auxiliary materials. The fertilizer is prepared from the following raw material components in parts by weight: 7-9 parts of seaweed, 5-7 parts of algae residues, 6-8 parts of microalgae residues, 4-6 parts of ascophyllum nodosum, 1-3 parts of Ecklonia kurome, 4-6 parts of kelp, 3-5 parts of gulfweed, 2-4 parts of Chewangzao, 2-4 parts of desert algae, 2-4 parts of Rhodomelaceae, 3-5 parts of fucus, 1-3 parts of enteromorpha, 1-3 parts of Ulva lactuca, 3-5 parts of Kappaphycus, 3-5 parts of brown algae, 2-4 parts of citrus peel residues, 1-3 parts of zeolite, 4-6 parts of shells and 4-6 parts of urea. According to the composite seaweed fertilizer and the preparation method thereof, compared with an organic fertilizer, thec omposite seaweed fertilizer use algae as main raw material, the cost can be effectively reduced, the environment optimization effect can be achieved, the manufacturing method changes a traditional evaporation and concentration process, energy consumption is reduced, and through the processes of drying, cooling, reacting, fermenting and the like, the composite seaweed fertilizer has the advantages that various nutrients in the algae are fully used, the cost is conveniently reduced, the application range of the seaweed fertilizer is widened, the environment is effectively protected and the like.