The invention relates to the field of novel organic fertilizers, and discloses a high-activity small-molecular carbon-rich fertilizer and a preparation method thereof. The high-activity small-molecular carbon-rich fertilizer is prepared from, by weight, 1 part of organic solid waste, 0.6-0.9 part of straw, 0.04-0.1 part of kieselguhr, 0.01-0.1 part of oyster shells and 0.1-0.5 part of wood dust. Compared with the prior art, the high-activity small-molecular carbon-rich fertilizer contains rich amino acids, dipeptide and polypeptide and small-molecular organic matter, does not contain heavy metals, hormones, ova, pathogens and the like and has the advantages of being harmless, small in molecule, high in activity, small in dosage, capable of saving manpower, small in specific gravity, looser and the like. Meanwhile, the high-activity small-molecular carbon-rich fertilizer has the obvious effects of improving soil, promoting plant growth and enhancing plant resistance, inhibiting plant pathogens and the like, and a series of agricultural problems caused by usage of chemical pesticides and chemical fertilizers are thoroughly solved.