The invention relates to a composite microbial fertilizer capable of preventing the vegetable root-knot nematode disease and a preparation method thereof, and belongs to the field of fertilizer production. The composite fertilizer is produced by the following steps: adding carbon containing plant powder and cereal protein powder into a decomposed organic fertilizer to prepare an organic substance, adding functional bacteria into the organic substance, and fully and evenly mixing to obtain the novel multi-resistance composite fertilizer. The functional bacteria can breed massively around the roots of vegetables and crops to form circular protective covers, thus the diseases caused by root-knot nematode are prevented effectively, a good ecological environment is created for the growth of vegetables, at the same time, the soil environment is improved, the soil hardening is avoided, the ventilation and oxygen content of soil are improved, the product quality and output are increased, and the fertilizer has the functions of pesticide and fertilizer. The organic substance content of the composite microbial fertilizer is not less than 50%, and the beneficial bacterium content is 6*10<9> CFU/g. The composite microbial fertilizer is easy to use, the fertilizing effect is high, the fertilizer only needs one application, labor is saved, and the environment is protected.