The invention discloses a carbon-based microbial organic fertilizer and a preparation method thereof. The organic fertilizer is prepared from the following components in parts by weight: 15-25 parts of biochar, 10-25 parts of ferric chloride, 1-5 parts of EM bacteria, 25-40 parts of cow dung, 25-35 parts of bran, 5-10 parts of citric acid, 10-15 parts of nano iron powder, 85-95 parts of distilledwater and 1-10 parts of honey. The preparation method is simple in preparation process and relatively low in cost; the fertilizer can be used for fertilization of land and crops such as fields, facility greenhouses, potted plants and heavy metal pollution, can effectively adjust the pH of facility soil, improve the soil structure and porosity, loosen the soil, promote accumulation and conversion of organic substances, reduce nitrate nitrogen and available phosphorus leaching loss of the soil, and increase the content of organic matters and N, P and K nutrients in the soil. The microbial activity can be improved, heavy metals in the soil can be effectively adsorbed, fixed and passivated, heavy metal pollution and continuous cropping obstacles of the soil can be repaired, and the yield and quality of crops can be improved.