The present invention discloses a carbon-based composite biological fertilizer. The carbon-based composite biological fertilizer is prepared from the following raw materials in parts by weight: 20-60parts of biochar, 10-30 parts of plant ash, 8-25 parts of medical stone powder, 3-15 parts of zeolite powder, 2-8 parts of potassium feldspar powder, 1-6 parts of ground phosphate rock, 15-45 parts ofhumic acid, 1-10 parts of potassium fulvate and 1-15 parts of photosynthetic nitrogen fixation composite bacteria. The carbon-based composite biological fertilizer gives full play to the respective advantages of photosynthetic nitrogen fixation composite bacteria, biochar, plant ash, medical stone powder, zeolite powder, potassium feldspar powder, ground phosphate rock, humic acid and potassium fulvic acid, not only realizes effective improvement and remediation of soil and improves the crop yield, but also is beneficial to promoting the development of green low-carbon agriculture. The invention also provides a preparation method of the carbon-based composite biological fertilizer, which is simple and convenient to operate and convenient for batch production. The invention also provides application of the carbon-based composite biological fertilizer, and the carbon-based composite biological fertilizer is compounded with one or more of decomposed manure, an organic fertilizer, slag, biomass pyrolysis residues or crop wastes according to different types of soil, so that the fertilizer efficiency is exerted.