The invention provides a fermented carbon-based bio-organic fertilizer and a preparation method thereof and relates to the technical field of preparation of bio-organic fertilizers. The fermented carbon-based bio-organic fertilizer is mainly prepared from, by mass, 10-18 parts of biomass charcoal, 3-8 parts of fish meal, 3-8 parts of bone meal, 5-9 parts of rice bran, 8-12 parts of vermiculite, 25-35 parts of common organic fertilizer, 60-80 parts of humus and 0.5-1 part of EM bacteria and biocontrol growth-promoting bacteria mixed according to the mass ratio of 1 to 1. The method comprises the following steps that 1, a fungicide is prepared and pretreated; 2, the carbon-based bio-organic fertilizer is prepared. The invention aims to prepare the carbon-based bio-organic fertilizer. Namely, the biomass charcoal, a functional microbe, the organic fertilizer and an organic substance including the rice bran, the bone meal, the fish meal or a cake fertilizer and the like are used as main raw materials, and a solid-state aerobiotic superficial layer fermentation technology is utilized to prepare the novel fertilizer having large functional microbe quantity, high activity and strong soil adaptability and effectively improving the soil fertility.