The invention discloses a composite microbial inoculant for preventing and treating tobacco black shank and a bio-organic fertilizer. The composite microbial inoculant is prepared from bacillus cereus QJ-1, aspergillus niger Ty-3, aspergillus fumigatus Ty-1, bacillus subtilis and a yeast, wherein the total bacteria count of the composite microbial inoculant is 5 hundred million cfu/g or above; the viable count ratio of bacillus cereus QJ-1 to aspergillus niger Ty-3 to aspergillus fumigatus Ty-1 to bacillus subtilis to the yeast is (2-4) to (2-4) to (0.5-1.5) to (0.5-1.5) to (1-3). According to the composite microbial inoculant provided by the invention, the microbial powder is mixed at a certain ratio, so that a synergistic effect can be achieved, a strong inhibiting effect is achieved on the growth of pathogenic bacteria of tobacco black shank, the colonization and growth of functional bacteria are promoted, the microecological balance of soil is regulated, and the tobacco black shank is inhibited.