The invention discloses a carbon-based compound enzyme fertilizer, which is prepared from the following raw materials in parts by weight: 1 to 80 parts of agriculture, forestry and livestock waste fermentation liquor or extracting solution, 0.1 to 10 parts of humic acid, 1 to 20 parts of amylase, 2 to 35 parts of invertase, 1 to 15 parts of protease, 3 to 30 parts of bacillus subtilis, 4 to 35 parts of saccharomycetes, 0.1 to 10 parts of chemical fertilizer containing carbon, nitrogen, phosphorus, potassium, sulfur, calcium and magnesium elements, 0.1-5 parts of a chemical fertilizer containing rare earth elements of iron, manganese, zinc and boron, and 10-35 parts of a multisource plant compound enzyme. The invention solves the problems of durability of enzyme fertilizer activity, comprehensiveness of nutrients and growth of crops in reverse environments (such as saline-alkali soil and the like), improves the fertilizer efficiency, activates the fertility in soil, and reduces the use amount of chemical fertilizer.