The invention discloses a carbon-based compound fertilizer containing probiotic organisms. The carbon-based compound fertilizer comprises biomass carbon black and probiotics, wherein the biomass carbon black is prepared by the following method: carrying out low-temperature carbonization on agricultural wastes as biomass raw materials to form porous biomass carbon black. The probiotics are prepared by the following method: carrying out amplification culture on beneficial microorganisms and fermenting to form probiotic liquid; and mixing and then carrying out solid-liquid separation and expansion drying to form the probiotics, wherein the beneficial microorganisms are selected from one or more of peanibacillus ploymyxa, trichoderma, nitrogen-fixing bacteria, root nodule bacteria, phosphate-solubilizing bacteria, potassium bacteria, cellulose decomposition bacteria, antibiotic-producing strain and photosynthetic bacteria. The carbon-based compound fertilizer disclosed by the invention is made of microporous biomass carbon, and thus the carbon-based compound fertilizer has extremely-strong adsorption capacity and favorable light absorbing and temperature increasing effects; in addition, the probiotics of the carbon-based compound fertilizer are high in cell viability; and the carbon-based compound fertilizer can be preserved at normal temperature for a long time, can be mixed, granulated and dried with other organic and inorganic fertilizers without being influenced and is remarkable in synergistic action.