The invention belongs to the field of agricultural planting, and particularly relates to a carbon-based bio-enzyme fertilizer and a preparation method thereof. The carbon-based bio-enzyme fertilizer comprises an organic fertilizer, biochar, wheat bran, enzymes, molasses and beneficial bacteria, wherein the organic fertilizer comprises organic materials, urea and calcium phosphate. The carbon-basedbio-enzyme fertilizer can increase the organic matter content of soil, promote the growth of microorganisms in soil, increase a total microorganism amount and effective microbial communities in the soil, increase the pH value of the soil and adjust the pH value of the soil; and the carbon-based bio-enzyme fertilizer improves the activity of protease and urease in the soil, so the activity of thesoil is enhanced, soil fertility is improved, soil continuity is maintained, the disease resistance of crops is enhanced, nutrients required by crop growth are provided, the yield of grain crops is increased, and the quality of the grain crops is improved.