The invention discloses a charcoal-based microbial soil conditioner. The charcoal-based microbial soil conditioner comprises, by weight, 80-85 parts of charcoal, 10-13 parts of a composite microbial flora and 1-2 parts of an oxidized starch adhesive, and the composite microbial flora comprises photosynthetic bacteria, actinomyces, lactic acid bacteria, microzyme, Bacillus subtilis and Bacillus thuringiensis. The invention also discloses a preparation method of the charcoal-based microbial soil conditioner. The combined effect of charcoal and microbes alleviates soil acidification, reduces the unit weight of soil and increases the permeability and the water content of soil; soil organic matter formation is promoted to improve the validity of mineral elements; and the abundance of microbes at the rhizosphere of crops is cultivated to improve the rhizospheric environment of plants in order to make pathogen microbes difficultly grow and breed, so the insect diseases of crops is reduced, and soil heavy metal pollution is alleviated and restored.