The invention discloses a water-soluble carbon enzyme granule fertilizer and a preparation method thereof. The water-soluble carbon enzyme granule fertilizer is prepared from, by weight, 5-10 parts of medical stone, 3-10 parts of dolomite, 15-20 parts of nitrogenous fertilizer, 10-20 parts of phosphatic fertilizer, 30-40 parts of potassic fertilizer, 4-25 parts of fulvic acid, 1-10 parts of concentrated molasses fermentation liquor, 0.1 part of carbon enzyme, 1 part of polyglutamic acid, 0.1 part of polyaspartic acid, 2 parts of chelated calcium, 0.5-1 part of chelated magnesium, 0.2-0.5 part of quick-acting boron, 0.2-0.5 part of chelated zinc and 0.3-0.5 part of chelated iron. The water-soluble carbon enzyme granule fertilizer is good in water solubility and high in organic matter content, and a granular structure can be easily formed; the chelated trace elements in the water-soluble carbon enzyme granule fertilizer can be easily absorbed by plants, improve fertilizer efficiency and have a powerful function and a lasting effect.